“Alignment bolts” are unnecessary
“the trans moves seperately from the transfer case so aligning it isnt as easy as everyone claims.”
How so? Are they not bolted together?
“Should the trans be in gear when attempting this?”
If you’re having problems with the spines engaging, it’s preferable for it to be in gear (1st) so that you can grab the output on the t-case and turn it back and forth to get the splines to engage.
Use a tape measure and measure your gap on the top and the gap on the bottom and adjust the angle the trans is sitting at to get the gaps equal.
The two obstacles you’re going to run into is getting the splines to engage and after that, getting the nose of the shaft to slide into the pilot bearing. Usually, neither of these are accomplished without vigorously rocking the works back and forth until they slide in. Sometimes vigorous profanity can help.