I hear ya,I've tried doing a few "weekend swaps" and only had one succeed--back then I had more than one vehicle on the road though,so it wasn't like I couldn't get to work if I failed at getting it done by Monday morning..
One truck I had,a 74K2500,I pulled a 454 out of it that had a loose wrist pin on a Saturday morning,took about 2 hrs--then I pulled a 400 SB out of a '77 K10 Suburban I bought for parts,had to remove all 6 busted exhaust manifold studs,re-tap them,and replace the flex plate,that had teeth missing..(why I was able to buy the Burb for $425!)..that took the rest of the day..
Next morning ,Sunday,I got up at 7 am and put the 400 SB in the truck,hooked everything up,and by noon I had it driveable-but if I didn't have the Burb for parts I'd have been S-O-L because I had to use many other things off it too,that would have been tough to find in a junkyard here..
As for your starter dilema,I'm kind of stumped..
A gear reduction starter isn't any different that I know of,I swapped one off a 6.5 diesel to my 6.2 with no problems,just had to use the front brace for the gear reduction starter,its slightly different than the one for the direct drive starter.--so it shouldn't matter which one your using..
I don't see how the bell housing can affect the starter engagement unless the starter drive gear hits it or something...to check that you may be able to put two long bolts in the bell housing and remove the rest ,and pull the bell housing,cross member & transfer case back far enough so it cant contact the starter, and try cranking it over (with the pink wire pulled off the injector pump so it wont fire up) and see if that lets it crank properly..you'll have to support the transmission & t-case with a jack to keep the input shaft lined up..
That might save you a lot of labor & time pulling it completely apart for nothing,if thats not the cause..and if it was,you may be able to correct the problem without having to drop everything..