I don't think you have to do major surgery to swap input gears. IIRC, you pull the input cover plate which is just a few fasteners and the input gear/bearing comes out. Been awhile since I had one apart. Either way, you should do that anyway and install a new input seal just as preventative maintenance. Nothing sucks more than getting it all in and seeing a drip between the trans and tcase a month later. Good point on the shift fork pads. Look out for bent forks from people yanking the levers when they don't want to shift easily.
You may be able to get the proper case if you don't want to swap gears by looking at a 91' K30. I'm pretty sure that was the only year the 4L80E came in a square body.
Either way, good luck! I just dropped a 4L80E from a school bus van and I will tell you what, that beast is heavy