Feels like a transmission issue. "01 4Runner Ltd is shaking like crazy on acceleration above 40 MPH and deceleration at almost any speed.One guy suggested it might just need tranny fluid but I can't find a spout for that.

Your tires are either need balancing or you have a broken belt in your tire

Hello,

If problem only occurs 'under power' sounds like a u-joint (driveline - rear wheel drive) or a cv-axle (front wheel drive). Check for excessive play, fluid, boot tear and breakage.

Most chances that the clutch is weak

I am surprised the AAMCO techs have no ideas about this. This "slipping" could be caused by the overdrive system having a mechanical problem (e.g. sticking solenoid, leaking seal) when trying to engage or disengage.
The overdrive solenoid locks the torque converter when activated, and releases when deactivated, both starting to happen when the vehicle is above about 40 mph and depending on what the vehicle is doing at the time (accelerating, decelerating or coasting). When you depress the accelerator and the solenoid is engaged at close to this speed, it should immediately release, and then re-engage when you stop accelerating, and you should immediately feel a light "bump" each time, not a "fish bite".

Likely a rotating part hitting a resonant frequency. It might be a universal joint on the drive shaft, a wheel out of balance or tire out of round. You might try lightly touching the brakes while maintaining the same speed. If it's something to do with tires or wheels, that would likely stop it. My first car would oscillate violently after hitting a bump in the road, due to a loose suspension part.

takes a long time to run the rediness test since there are 6 different tests to complete...

PROCEDURE 1
EVAPORATIVE EMISSION SYSTEM LEAK MONITOR
Inspection Conditions
Engine coolant temperature: 30°C (75°F) or less (The engine is stopped before the test drive is started).
Atmospheric temperature: 5 - 30°C (41 - 113°F).
Condition of A/T: Selector lever D range.
Fuel remained in fuel tank: 30 - 50% is recommended.
Time required: 16 minutes or less after started the engine.
Drive cycle pattern: One trip monitor (from start to ignition switch to "LOCK" (OFF) position. Well be completed while traveling with the following drive cycle pattern.
Test Procedure
Engine: start.
Accelerate until the vehicle speed is 89 km/h (55 mph) or more.
While keeping the accelerator pedal opening degree constant, keep the vehicle speed at 89 km/h (55 mph) or more and travel for 16 minutes.
Return the vehicle to the shop, then turn the ignition switch to "LOCK" (OFF) position.

PROCEDURE 2
FUEL TRIM MONITOR
Drive Cycle Pattern
Inspection Conditions
Engine coolant temperature: 100°C (212°F) or less.
Atmospheric temperature: -10 - 60°C (14 - 140°F).
Condition of A/T: Selector lever D range.
Time required: 30 minutes or more.
Drive cycle pattern: One trip monitor (from start to ignition switch to "LOCK" (OFF) position). Will be completed while traveling with the following drive cycle pattern.
Test Procedure
Engine: start.
Accelerate until the vehicle speed is 89 km/h (55 mph) or more.
While keeping the accelerator pedal opening degree constant, keep the vehicle speed at 89 km/h (55 mph) or more and travel for 30 minutes.
Return the vehicle to the shop, then turn the ignition switch to "LOCK" (OFF) position

PROCEDURE 3
CATALYTIC CONVERTER MONITOR
Drive Cycle Pattern
Inspection Conditions
Atmospheric temperature: -10°C (14°F) or more.
Condition of A/T: Selector lever D range.
Engine coolant temperature: Not set.
Time required: 16 minutes or more.
Drive cycle pattern: One trip monitor (from start to ignition switch to "LOCK" (OFF) position). Will be completed while traveling with the following drive cycle pattern.
Test Procedure
Engine: start.
Accelerate until the vehicle speed is 89 km/h (55 mph) or more.
Travel for 300 seconds or more while keeping the vehicle speed at 89 km/h (55 mph) or more.
Decelerate until the vehicle speed is within 80 km/h (50 mph) or less.
While traveling at 56 - 80 km/h (35 - 50 mph) for 10 minutes or more, fully close the throttle at least once in 2 minutes and decelerate for 10 seconds or more.
Do not repeat deceleration too often.
Vehicle speed may go below 56 km/h (35 mph) after the deceleration.
Stopping and braking are permitted. (If stopped or drive at 56 km/h (35 mph) or less for more than 5 minutes the monitoring may be stopped. In this case please restart monitoring from the beginning.)
After completing the above deceleration, bring the vehicle speed back to 56 - 80 km/h (35 - 50 mph) and keep it in the range until starting the deceleration again.
Repeat the above deceleration at least 5 times.
Return the vehicle to the shop, then turn the ignition switch to "LOCK" (OFF) position

PROCEDURE 4
HEATED OXYGEN SENSOR MONITOR
Drive Cycle Pattern
Inspection Conditions
Engine coolant temperature: 100°C (212°F) or more.
Atmospheric temperature: -10°C - 60°C (14 - 140°F) or more.
Condition of A/T: Selector lever D range.
Time required: 16 minutes or more.
Drive cycle pattern: One trip monitor (from start to ignition switch to "LOCK" (OFF) position). Will be completed while traveling with the following drive cycle pattern.
Test Procedure
Engine: start.
Accelerate until the vehicle speed is 56 - 80 km/h (35 - 50 mph).
While keeping the accelerator pedal opening degree constant, keep the vehicle speed at 56 - 80 km/h (35 - 50 mph) and travel for 16 minutes or more.
Stopping and braking during this operation are permitted. Keep the accelerator opening degree constant for 1 minute or more after each acceleration.
Return the vehicle to the shop, then turn the ignition switch to "LOCK" (OFF) position

PROCEDURE 5
EXHAUST GAS RECIRCULATION (EGR) SYSTEM MONITOR
Drive Cycle Pattern
Inspection Conditions
Engine coolant temperature: 100°C (212°F) or less.
Atmospheric temperature: 5 - 60°C (41 - 140°F).
A/C switch: OFF.
Condition of A/T: Selector lever D range.
Time required: 16 minutes or more.
Drive cycle pattern: One trip monitor (from start to ignition switch to "LOCK" (OFF) position). Will be completed while traveling with the following drive cycle pattern.
Test Procedure
Engine: start.
Accelerate until the vehicle speed is 56 - 80 km/h (35 - 50 mph).
While traveling 16 minutes or more at 56 - 80 km/h (35 - 50 mph) with engine speed 2,000 r/min or above, fully close the throttle at decelerate for 5 seconds or more until the engine speed reaches 1,000 r/min or under.
Do not repeat deceleration too often.
Stopping and braking are permitted (Rapid deceleration and sharp steering are not permitted).
After completing the deceleration, bring the vehicle speed back to 56 - 80 km/h (35 - 50 mph) and keep it in the range until starting the deceleration again.
Repeat the above deceleration at least 8 times by fully closing the throttle valve.
Return the vehicle to the shop, then turn the ignition switch to "LOCK" (OFF) position

PROCEDURE 6
OTHER MONITOR (Main Components, Sensors & Switches, Wire Breakage & Short Circuit)
Drive Cycle Pattern
Inspection Conditions
Engine coolant temperature:
100°C (212°F) or less (Except engine coolant temperature sensor monitoring).
30°C (86°F) or less (Engine coolant temperature sensor monitoring).
Atmospheric temperature:
5°C (41°F) or more (Except engine coolant temperature sensor monitoring).
-10°C (14°F) or less (Engine coolant temperature sensor monitoring).
Condition of A/T: Selector lever D range.
Time required: 21 minutes or more.
Drive cycle pattern: One trip monitor (from start to ignition switch to "LOCK" (OFF) position). Will be completed while traveling with the following drive cycle pattern.
Test Procedure
Engine: start
Accelerate until the vehicle speed is 56 km/h (35 mph) or more.
While keeping the accelerator pedal opening degree constant, keep the vehicle speed at 56 km/h (35 mph) or more and travel for 16 minutes or more.
Return the vehicle to the shop.
After stopping the vehicle, continue idling for 5 minutes, and then turn the ignition switch to the "LOCK" (OFF) position. Moreover, the vehicle should be set to the following conditions for idling.
A/C switch: OFF
Lights and all accessories: OFF
Transmission: Neutral

I would say you should definitely do an alignment. Fixes it 9/10, along with the balancing of course. And, there is always the possibility of a worn tire being the issue.

Change the universal joints on the drive shaft.

Other problems can be

drive train misalignment
Transmission problems

if your vehicle only vibrates at speeds above a certain point the most likely cause of the issue is a tire balance issue. just make sure it doesn't matter if you accelerating or decelerating the vehicle just vibrates after a certain speed, and if this is the case take it to a tire shop and have them check the balance. shouldn't cost more than like 40 bucks.

Sounds like a bad torque converter. When the torque converter is engaged, it's not "whirring" it's on decel or freewheel that it "whirs".Did you check fluid level and color?