Like what was suggested earlier, I would also recommend using the Allison if you have access to one. Then you can use the newer NV261/263 transfer case and you could use all of the aftermarket power mods available for the engine.
The intercooler installation can be and has been done successfully, as shown in the Conversion Guide. No problems in the 5+ years since I did mine. I know of a couple C/K conversion projects that didn't use an intercooler at all. The engine will work without one, but it limits power, which might not be a problem if you use the 4L80 and keep the power moderate.
Jim