I swapped a 04 trans into my 98, I used just the 04 transmission. The clutch, flywheel, shifter and stub were all from my 98. It now pops out first gear and makes a weird noise. It gets louder with speed and doesn’t matter much if the clutch is engaged or not.

 

You swapped in an M5OD-R1HD, manual trans, 2001-2011 4.0l Rangers/B4000s

Your 1998 had an M5OD-R1

The shifter is different between these two transmissions, picture here: https://www.therangerstation.com/Mag...D-R1HD/m14.JPG

Other than that and an extra bolt hole on bell housing they are the same transmission inside, so plug and play

If it was a used transmission then it most likely already had the popping out of 1st issue and was making a noise, nothing you did when doing the swap
What did the old trans fluid look like?
These do use Ford ATF, Mercon V or synthetic equivalent

If you got if from a wrecking yard they often will warranty these with an exchange, not money back

Here is the whole article on doing this swap: https://www.therangerstation.com/tec...h-a-m5od-r1hd/