4Runner Jerking after Shifting Gears

Hello 4runner enthusiasts. I have a 1994 3.0, 4x4, 5spd with 230k miles, which I have owned for 11 years/45k miles. The problem first started where I would shift into 3rd gear and upon completing the shift, she would give a series of 3-4 quick jerks/bucks before settling in and accelerating normally. This would only happen in 3rd gear. However, this has now progressed to where it happens when shifting into 1st, 2nd and 4th gears as well.

Some observations:
-It does not always happen every gear shift event, but is most common going into 3rd
-1st and 4th gear jerking is less common and 5th shifts smoothly.
-Happens regardless if engine is cold or warm
-Jerking only happens for a couple seconds and RPMs stay relatively stable, maybe a slight drop but they are not running away like a slipped clutch
-I do not hear or feel any grinding noises
-Definitely not a skill issue as I have owned her for nearly a decade before this started happening.
-There has been no transmission work done since I've owned her and previous service records were not provided by last owner
-During an alignment a couple weeks ago, the mechanic noticed a worn u-joint in the rear driveshaft. I was hoping that might be the problem, so replaced both ends of rear driveshaft with Spicer u-joints....but this did not result in any noticeable change in driving.
-Fluid levels in transfer case and differentials are SAT.

I've searched this forum and the internet for something similiar and not finding anything. Does anyone have any insight on what could cause this? Or ideas for troubleshooting to narrow this down?
Any help would be much appreciated. Thanks!

 

Shooting from the hip here, but possibly a dirty MAF (might be an 'air flow meter' in your case)? I once had an '88 22R-E with a sticky air flow meter that had similar symptoms. It had a 'butterfly' type regulator, and I diagnosed it by spraying lube on the upper and lower pivot points of that regulator. The unit looks similar to this.

 

When was the last tuneup? Spark plugs, wires, cap, rotor, air filter and fuel filter.

 

^agree