Knock, Knock? My tower is making a knocking noise, which is followed by slow performance and eventually shutting down. Any clue what is going on?

Well the knock sensor does not make any noise. It senses the vibration in the engine if there is a spark knock to let the computer know to slow down the spark timing.
You probably have a weak piston or lifter or rod bearing making the noise.

Listen to the engine, if the noise is down low it is rod if it is up high it is valves. IF it is rod knock it will eventually throw the rod.

TROUBLESHOOTING ENGINE NOISES
A KNOCKING SOUND IN THE ENGINE IS MOST LIKELY CAUSED BY ONE OF THE FOLLOWING
1. PISTON SLAP: Makes a sharp metallic noise. Idle engine and short out each cylinder plug. The noise will disappear when plug with bad piston is shorted. Noise will also disappear at acceleration. This can be caused by worn or out of round cylinder, or broken piston ring. Correct problem by re-boring cylinder and/or replacing piston.
2. VALVE NOISE: Makes clicking or rattle noise. Caused by excessive wear on valve stem or lifter, out of adjustment, or stuck valve. Correct by adjusting valve clearance, replace worn valve or lifter, regrind cam, replace valve guide and /or valve. A stuck valve can sometimes be loosened by passing oil through the carburetor while engine is running.

3. ROD BEARING KNOCK: Makes sharp metallic noise similar to a piston slap. Detection is opposite of piston slap. Rod knock is not heard at idle. Knock becomes louder as engine speed is increased. Caused by excessive rod bearing clearance. Correct by adjusting rod bearing clearance to .0015 inches by removing shims. May require re-pouring rod bearing.
4. REAR MAIN BEARING KNOCK: Makes dull knocking or thud noise. Detected at speeds between 20 and 50 MPH. Knock will normally decrease or disappear while pulling or decelerating. Noise will be detected the loudest at normal driving speed, when not pulling or decelerating. Correct by adjusting bearing clearance to .001 to .0015 inches. If knock is excessive, crank should be checked for out of roundness. May need to re-pour all main bearings to correct.
5. TIMING GEAR KNOCK: usually the most difficult to diagnose. If gear is loose or badly worn it will knock in all ranges. Run engine slightly above idle speed. Slowly open and close throttle. Knock will continue to be present, but just as engine slows down knock will become a slight rattle. Remove timing pin and reinsert into timing hole on timing gear cover. Press timing pin tightly against timing gear and accelerate slightly above idle. Knock will significantly be reduced or disappear. Correct by replacing both timing gear and crank gear as a matched set. The two gears should have a backlash clearance of .003 to .004. If more than .009 inch backlash, an oversize (.005) timing gear should be installed.
6. WRIST PIN SLAP: This can not be detected by shorting out the cylinder plugs. Rapidly accelerate and decelerate the engine speed. The engine will pass through a certain speed range when the wrist pin will rattle at about the same pitch as a valve tappet noise. This can be corrected by installing a new wrist pin bushing in the rod or new wrist pin f badly worn. Wrist pin should fit the piston and connecting rod with a tight metal to metal fit. The pin can be pushed into the piston and rod with a slight pressure of the hand. Pin to rod clearance is .0003 to .0005 inches.

A KNOCKING SOUND IN THE ENGINE IS MOST LIKELY CAUSED BY ONE OF THE FOLLOWING
1. PISTON SLAP: Makes a sharp metallic noise. Idle engine and short out each cylinder plug. The noise will disappear when plug with bad piston is shorted. Noise will also disappear at acceleration. This can be caused by worn or out of round cylinder, or broken piston ring. Correct problem by re-boring cylinder and/or replacing piston.
2. VALVE NOISE: Makes clicking or rattle noise. Caused by excessive wear on valve stem or lifter, out of adjustment, or stuck valve. Correct by adjusting valve clearance, replace worn valve or lifter, regrind cam, replace valve guide and /or valve. A stuck valve can sometimes be loosened by passing oil through the carburetor while engine is running.

3. ROD BEARING KNOCK: Makes sharp metallic noise similar to a piston slap. Detection is opposite of piston slap. Rod knock is not heard at idle. Knock becomes louder as engine speed is increased. Caused by excessive rod bearing clearance. Correct by adjusting rod bearing clearance to .0015 inches by removing shims. May require re-pouring rod bearing.
4. REAR MAIN BEARING KNOCK: Makes dull knocking or thud noise. Detected at speeds between 20 and 50 MPH. Knock will normally decrease or disappear while pulling or decelerating. Noise will be detected the loudest at normal driving speed, when not pulling or decelerating. Correct by adjusting bearing clearance to .001 to .0015 inches. If knock is excessive, crank should be checked for out of roundness. May need to re-pour all main bearings to correct.
5. TIMING GEAR KNOCK: usually the most difficult to diagnose. If gear is loose or badly worn it will knock in all ranges. Run engine slightly above idle speed. Slowly open and close throttle. Knock will continue to be present, but just as engine slows down knock will become a slight rattle. Remove timing pin and reinsert into timing hole on timing gear cover. Press timing pin tightly against timing gear and accelerate slightly above idle. Knock will significantly be reduced or disappear. Correct by replacing both timing gear and crank gear as a matched set. The two gears should have a backlash clearance of .003 to .004. If more than .009 inch backlash, an oversize (.005) timing gear should be installed.
6. WRIST PIN SLAP: This can not be detected by shorting out the cylinder plugs. Rapidly accelerate and decelerate the engine speed. The engine will pass through a certain speed range when the wrist pin will rattle at about the same pitch as a valve tappet noise. This can be corrected by installing a new wrist pin bushing in the rod or new wrist pin f badly worn. Wrist pin should fit the piston and connecting rod with a tight metal to metal fit. The pin can be pushed into the piston and rod with a slight pressure of the hand. Pin to rod clearance is .0003 to .0005 inches.

A KNOCKING SOUND IN THE ENGINE IS MOST LIKELY CAUSED BY ONE OF THE FOLLOWING
1. PISTON SLAP: Makes a sharp metallic noise. Idle engine and short out each cylinder plug. The noise will disappear when plug with bad piston is shorted. Noise will also disappear at acceleration. This can be caused by worn or out of round cylinder, or broken piston ring. Correct problem by re-boring cylinder and/or replacing piston.
2. VALVE NOISE: Makes clicking or rattle noise. Caused by excessive wear on valve stem or lifter, out of adjustment, or stuck valve. Correct by adjusting valve clearance, replace worn valve or lifter, regrind cam, replace valve guide and /or valve. A stuck valve can sometimes be loosened by passing oil through the carburetor while engine is running.

3. ROD BEARING KNOCK: Makes sharp metallic noise similar to a piston slap. Detection is opposite of piston slap. Rod knock is not heard at idle. Knock becomes louder as engine speed is increased. Caused by excessive rod bearing clearance. Correct by adjusting rod bearing clearance to .0015 inches by removing shims. May require re-pouring rod bearing.
4. REAR MAIN BEARING KNOCK: Makes dull knocking or thud noise. Detected at speeds between 20 and 50 MPH. Knock will normally decrease or disappear while pulling or decelerating. Noise will be detected the loudest at normal driving speed, when not pulling or decelerating. Correct by adjusting bearing clearance to .001 to .0015 inches. If knock is excessive, crank should be checked for out of roundness. May need to re-pour all main bearings to correct.
5. TIMING GEAR KNOCK: usually the most difficult to diagnose. If gear is loose or badly worn it will knock in all ranges. Run engine slightly above idle speed. Slowly open and close throttle. Knock will continue to be present, but just as engine slows down knock will become a slight rattle. Remove timing pin and reinsert into timing hole on timing gear cover. Press timing pin tightly against timing gear and accelerate slightly above idle. Knock will significantly be reduced or disappear. Correct by replacing both timing gear and crank gear as a matched set. The two gears should have a backlash clearance of .003 to .004. If more than .009 inch backlash, an oversize (.005) timing gear should be installed.
6. WRIST PIN SLAP: This can not be detected by shorting out the cylinder plugs. Rapidly accelerate and decelerate the engine speed. The engine will pass through a certain speed range when the wrist pin will rattle at about the same pitch as a valve tappet noise. This can be corrected by installing a new wrist pin bushing in the rod or new wrist pin f badly worn. Wrist pin should fit the piston and connecting rod with a tight metal to metal fit. The pin can be pushed into the piston and rod with a slight pressure of the hand. Pin to rod clearance is .0003 to .0005 inches.

Duplicate question.
I doubt the sensor would make the engine stop running. The computer would slow down the spark timing to prevent engine knock, but not shut it off.

Hi, Sam_kellick I would love to help you with your engine or chassis noise but I just loaned my brand new pair of listening ears to your local dealer's chief technician so he could take your bike for a test ride and give you his professional opinion and estimate about your noise and repair cost. If you are a little short on "DRACHMA" and a Dealership is not on your list of fun places to visit then perhaps the list below will help soothe your worried mind so you can make an informed decision.
1. Bearings---SCREECH
2. Belts---CHIRP
3. Brake Rotors---BUZZ
4. Chains---RATTLE
5. Clutches---CHATTER
6. Cylinders---PING
7. Fronk Forks---Plunk
8. Gears---WHINE
9. Head Gasket---HISS
10. Hydraulic Lifters---TAP
11. Pistons---SLAP
12. Rear Shocks---SQUEAK
13. Shifting Trans---CLUNK
14. Solid Lifters---TICK
15. Starters---CLICK
16. Connecting Rods Go---KNOCK-KNOCK---who's there, it's me "*****"
For more information about your issue and valuable "FREE" downloads that you will need please click on the links below. Good luck and have a nice day.
Strange Knocking Noise In First Gear Clutch Drag
How to diagnose problem by the noises your bike makes
http://gigi600.altervista.org/immagini/xt125r/XT%20125%202005_service.pdf
OEM parts for Yamaha
http://mybikemanuals.com/yamaha/yamaha-xt-owners-manuals

Btw, I’m available to help over the phone in case u need at https://www.6ya.com/expert/gregg_c0ec1df182c7330e

The knock sensor code does not always mean the sensor is faulty.
The sensor picks up noise and vibration in the engine such as a spark knock would generate, and the computer slows down the spark timing to fix it. If the noise or vibration continues, the code is set.
Could be a noisy valve, or a problem with the crankshaft or other component.

Your not going to here any knock from the engine the knock sensor detects detonation which is not detectable with the human ear. if you want to test the knock sensor you can tap the side of the block the engine should stumble for a couple of seconds if it does not change then the way the engine runs then the knock sensor is defective or hase buildup iside the engine and you will need to do a top engine clean. if you want instructions on how to do this just post another post to this reply This happens on engines that ave high mileage or acar that runs low grade like regular.

THROW OUT BEARING IS MAKING THE KNOCK NOISE , I AM REPAIRING A 1991 L98 CONV. RIGHT NOW FOR THE SAME ISSUE!

Btw, I’m available to help over the phone in case u need at https://www.6ya.com/expert/craig_a14a43e01fd0835a