Update: The trans and transfer case are back in and are sealed with new gaskets. The new Y pipe fit nicely until it came time to install the clutch slave. The way the old bell housing and clutch slave mounted in comparison to the new y pipe caused all kinds of interference.
The first problem was I needed a longer clutch hose in order to avoid the line sitting on the exhaust. This proved to be harder than expected because I couldn't find a longer line with the correct m12x1.0 fittings. Instead I had to order a longer line with 1/4 fittings and then use two 1/4 to m12 adapters in order to make everything connect.
The next problem that came up was the clutch slave inlet hole was directly in line with the exhaust pipe and only about 2" away, so I flipped the slave 180 degrees but then the inlet hole was directly inline with my oil filter. Finally I had the idea to swap the bleed screw and the inlet hole since the bleed screw doesn't require much clearance and as far as I can tell there is no difference between the inlet and bleed screw holes. The holes are identical, both hold the same pressure in application, and it gave me the clearance I needed.
The final problem was bleeding the clutch. It was a pain in the ass. After many tries of conventional bleeding (hold the pedal down, release the bleeder, tighten the bleeder, release the pedal) we finally got it bled by actuating the slave cylinder by hand nice and slow until the air trapped in the slave had escaped up through the master and out the fill cap. A quick regular bleed after that and I had clutch pressure.
The pile of parts is getting small now. I think I have to get the driveshafts back in, double check the wires/cables running to the trans and tcase, move the back half of the exhaust over to the passenger side and attach it to the y pipe, double check all my fluids, and I may be just about there.