You would be surprised about how poorly that can locate a transmission. We did an engine swap with a DIY adapter plate before, and we thought the clutch and pilot bearing would hold everything aligned while we bolted it down. Didn't take long to cook the input bearing in the transmission because of alignment issues.
Flip the engine on its face, so the flywheel end is pointing up. Take the transfercase off the transmission to make it lighter and less awkward, and then set the transmission down into engine with the clutch and pilot bearing installed. You will find that you will be able to slide the transmission left/right/up/down wayyy more than you'd think you should be able to despite the shaft being rigidly locked in the engine.
My recommendation would be to insert the transmission into the engine as described above, and then slide the transmission around with a dial indicator on the X and Y axis. Find the maximum amount the transmission will slide around in each axis, and then carefully set it in the middle of those distances. That should minimize loads on the input bearing.