NEED help with aw4 tranny

I have a 94 xj 4.0 ho aw4 np231 3.5 budget boost. I recently swapped motors and in my exhaustion I guess I didn't get motor to tranny tight enough and they separated on the way to the river. Got it back together and had no gears. Get it back home take to my tranny guy and we pull it apart and find only the pump was damaged, so we swapped them and I put the tranny in. First test in the drive way worked fine. Added little more fluid and apparently over filled it. Drained little out then no reading on the dip stick. The whole time I'm playing with the fluid it takes 1500 rpms to get it to engage a gear and struggles to move. Finally got fluid level correct and still does the same thing like taking awhile before getting in gear. Right now I'm just looking for a direction to run my jeep.
Anything can help. Thanks

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How much did you put in it? How are you reading the fluid level on the dipstick? should be completely warm (20Mins of driving) and in neutral or park (cant remeber which) when reading it.

Sounds like there's still not enough fluid in it from what you're describing; its not like reading your oil dipstick

I believe before taking a reading the vehicle should be warm and you should cycle through all gears before placing it in park and taking the reading. Also on level ground.

Also is there any noise associated with the engagement of a gear?

I've gpne through all the steps filling the tranny. There's not any noise when shifting around between park and drive.

Sounds like the torque converter is not seated in to the pump correctly. When motor and trans separated, converter is still attached to flywheel. then you just tightened up the bolts but didn't re-seat converter back onto pump housing.

I have pulled the tranny out and swapped pumps and then seated th tc.

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Make sure you don't have any leaks in the fluid lines.

If it's not that, I'd bet you are about to replace the trans... mine started doing this shortly before it stopped working at all and started making some really ugly noises even in park/neutral.