The only real room issue is your short wheel base.
That means using cv joints or a drive shaft that probably costs more than the truck did.
Your is 2" longer and 100lbs heavier and possibly taller than mine is. My reduction is 2.14. The good creeper is not what I need. It is truely the ability to move period. Ever get stuck in the middle of a hill because you do not have what it takes to make the grade? 216 0r 454 becomes irrelevent at altitudes above 10,000 feet because they both become gutless.
Getting back to the tranny, My vent I think is the same as yours. Right rear corner on top. A simple pipe elbow solves that because even at 90 degrees its still at the top. 90 degrees would make the mounts even easier. 2 eyes on top of the frame rails, between the cab and box for a 1 inch bar that will go thru the mount hole on the back corner. Then bend a bar to fit thru the bottom. The front mount being rotational just sits on any standard cross member. Any spicer manual I've seen states that the main shaft seals will leak if overfilled.
Clocking at 90 degrees would be the same as severely overfilled.
Clocking at 90 degrees would actually make the shift linkage easier. Instaed of being on top the rods would be on the left side just like any standard floor shifter. The factory type shifter puts the rods and shifter directly above the driveline. Since the top of the aux box would be up against the floor. The shifter and its mounting bracket would actually have to be above the floor. These need no special shifter. Any 3 speed floor shifter works. Factory installed van shifters work great if you can find one. I dumped the bench seat and but in buckets to make room for mine.
If I clock the aux box at 90 degrees the seals are in lube always, at about 60 degrees they would be above the lube. My biggest concern is getting enough lube at the counter shaft. Some spicer boxes have the counter shaft completely under lube. Yours and mine would normally be filled to mid shaft. If the lube level on the counter shaft is lower, wouldn't that be somewhat like running without sufficient lubrication?