Has a code of mutiple misfire, 3 plugs in back burned off. also has a badly leaking exhaust manifold gasket would that cause the misfire?

you have addressed most of the things that cause these codes

https://www.google.com/search?q=2006+Ford+Mustang+P0106+and+P2195


MAP Sensor (as opposed to MAF)
P0106 Manifold Absolute Pressure/Barometric Pressure Circuit Range/Performance O2 Sensor P2195 O2 Sensor Signal Stuck Lean When the O2 sensor reports lean, it is dumping extra fuel which causes carbon fouling. This takes a while to burn off or you can use an 'Extreme Clean' type fuel system cleaner.

https://www.cjponyparts.com/resources/mustang-dtc-codes

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That could be a sign of a blown head gasket check and make sure the car is not over heating if so that may be the case.

check your valve cover gasket its fairly easy to replace

P0304 Code indicates a misfire on cylinder 4
Most likely causes for this are bad wire, bad spark plug, bad coil(s) or bad dist cap if so equiped.
A vacuum leak can also cause a misfire.
Seeing the vehicle is going on 13 years old replacing the wires and the plugs would be a good place to start, and could be the solution

could also be a bad coil or ignition wire

Code P0303 means that there is a misfire detected on cylinder #3. This could becaused by anything from a worn out spark plug to a blown cylinder head gasket, a faulty fuel injector, a bad ignition coil, or a leaking intake manifold gasket. I have also seen this type of code caused by clogged-up EGR ports in the intake manifold on certain engines. "Freeze Frame Data" stored in your Engine computer along with the fault code is designed to help identify what engine conditions (high speed/slow speed, heavy load/light load, etc.) are producing the misfire. This helps a lot in identifying exactly what is causing the cylinder to misfire.

One way to eliminate some of the possible causes is to swap parts with another cylinder to see if the code changes.

If you have "Coil-On-Plug" ignition, you can swap the coil on #3 cylinder with the coil on #4 Cylinder and swap the #3 spark plug with the #2 spark plug. Then clear the codes and drive the car till the Check Engine (or Service Engine Soon) light comes back on.

If it still gives you P0303, then it is not being caused by the plug or the coil. It could be any of the other possible causes listed above.
If it now gives you P304, replace the bad ignition coil that is now on #4 cylinder.
If it now gives you P302, Then replacement of all the spark plugs is recommended.

Misfires across all 6 cylinders could indicate the following:


Priority Action Part Type Cause 1 Inspect Wireset Worn, Damaged or Faulty Spark Plug Wire(s). 2 Inspect Distributor Cap Loose, Burned or Cracked Distributor Cap. 3 Inspect Distributor Cap and Rotor Kit Loose, Burned or Cracked Distributor Cap and Rotor. 6 Inspect Spark Plug Fouled, Damaged, Broken, or Incorrectly Gapped Spark Plug(s). 7 Inspect Coil - Ignition Faulty Ignition Coil. 8 Inspect Condenser-Ignition Faulty Condenser-Ignition. 9 Inspect Point Set Burned, Worn or Incorrectly Set Ignition Points. 15 Inspect Timing Specification Incorrect Ignition Timing. 19 Inspect Fuel Injector Dirty or Worn Fuel Injectors. 21 Inspect Intake Manifold Gasket Leaking, Worn, or Damaged Intake Manifold Gasket. 22 Inspect Distributor Worn, Damaged or Faulty Distributor. 24 Inspect Valve Burned, Worn, or Sticking Exhaust Valves.

CODE P1313 MISFIRE CATALYST DAMAGE BANK 1 CODE P1314 MISFIRE CATALYST DAMAGE BANK 2 COULD BE MANY THINGS THAT CAUSE THAT PROBLEM.FAULTY EGR VALVE FAULTY MASS AIR FLOW SENSOR OR BAD COOLANT SENSOR BAD O2 SENSORS.LEAKING INTAKE MANIFOLD LEAKING EXHAUST PIPE OR EXHAUST MANIFOLD.

replace the coil it is most likely bad. observe the engine at night or in a dark environment and proceed to use a spray bottle to lightly coat the coil pack for that cylinder number 3 and if you see an arc at the coil or any where else this will confirm a bad coil but even if you don't see any arcing it still may be a weak coil.