Many a members can answer your question with much more knowledge and reasoning than I can, but I'll throw what I think I know into the ring.
Engines and transmissions are sized according to the size of the bus they will be used in. An 8.3 is a damn big engine for a mini to mid size bus.
Per the transmissions, the two you mentioned are two pretty different animals. The MT643 (I have one) is a mechanical transmission. The only thing electrical about it would be the shift modulator, which is activated by an Engine Control Module (computer). If the engine doesn't have a computer, the modulator will be mechanical. The main issue with the MT643 (and AT545 found in smaller rigs) is that they only have four gears, and the aforementioned modulator is a known issue in those transmissions. With so few gears, it's got a big range between gears, so you have less performance and your tranny works harder.
The 3060 (3000 series) is a great transmission, but again, rated for larger vehicles. The 1000 and 2000 series are the little and baby brothers of the 3000. All three of these are computerized and electrical. They generally have 5, sometimes 6 gears giving you better mpg, tighter gearing and the tranny doesn't have to work so hard. Think of doing the same job with 4 people vs 5 or 6.
So, if you're looking at a smaller bus (not full size), you're likely to get a smaller engine 5.9, 6.7, 7.3L and transmission, MT545 (avoid), MT643 or maybe a 1000 or 2000 Allison series.
What's best for you really depends on what you are wanting to do with your bus. Are you going to live in it full time and travel a lot? Are you going to be venturing over long grades and at altitude? Or, is it more of a weekend use with short drives and relatively low engine loads (flat roads)? Speaking of roads, are they always going to be paved, maintained dirt or "Hold on Martha, it's going to get bumpy!"?
All this can make a real difference in what vehicle, engine and tranny you're going to try and find.
Sharing these details will help others give you better responses.
Best of luck.