I was re reading your post and something you said tripped a memory cell. If I understood you correctly you said you pulled the trans out of the vehicle and put it back in. If so I presume you disconnected the clutch slave cylinder. If this is correct, Did you bleed the clutch when you put it back in?
Now on to a couple of more questions. Do you have difficulty moving the shifter from neutral to any gear position? Try this, idle in neutral press on the clutch and shift into 3rd gear. Keep holding the clutch pedal down. shift to neutral, Not place the shifter into reverse and then let the clutch out.
If you had problems shifting into any of the gears from neutral with the clutch pedal fully depressed then you may have a clutch problem. The hydraulic clutch in a B2 is a pain when it comes to bleeding the hydraulic clutch. You may not see any air coming out and think it is good but they are notorious for trapping air then when you step on the pedal it doesn't press the throw out bearing fully causing the clutch to not fully release. When this happens you have a very hard time getting in gear from neutral because the clutch won't fully release.
If you have this problem it may very well act jumpy as maybe the trans did not go fully in gear because of the clutch dragging. Now, as the torque builds the trans slips into neutral because it wouldn't go all the way in gear.
This may or may not be what is going on! Then again it could describe your situation. I am just throwing out general thoughts. Read what I wrote and let me know if any of them things apply.