Not lining up
 

I have a 96 s10 4wd with the 4L60E trans. earlier this month we swapped out the transmission for a junk yard one. when the test drive came i shifted from park into reverse and the light to tell you what gear youre in moved to R. Then i went to neutral and it stayed at R, then i went to OD and it moved no N and kept doing that all the way to 1st where it stayed at 2. when i went up from 1 to 2 it stayed at to then shift up to D went to D and shift to OD went to OD etc. etc. why is it doing that? and could that cause any problems?

You'll have to adjust the shifter linkage.

but would it be a problem in the future if i didnt adjust anything and just let it be? haha

If your indicator light shows you in Neutral while you're really in Reverse or Drive, etc... could be disastrous.

Correctly adjusting the linkage will take you five minutes.

okay would i have to go into the pan to adjust it then?

It's external.... you disconnected/reconnected it when you changed the transmission.