I'm in the same boat (bus?) as you, trying to find the "right" combination that's also available at a reasonable price.
This is all based on what I've read on the forums and the limited amount of buses that I've seen (and their on-road performance).
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ENGINE & FUEL
You'll want diesel unless you're going with a long van, or maybe some cutaway buses (also very small). Anything larger and you'll want a diesel.
You are right about the engines - DT466 is the most recommended engine I've seen on here, with some people putting the cummins up there with it, others pushing it to second place. The DT444 isn't as good as the 466, but will suffice with lower power applications.
The CAT 3126 is either one of the best or worst engines depending on which threads you read. They're either incredibly much more expensive to repair compared to cummins/DT, or they are only a bit more to repair. It is true that CAT mechanics are a bit more uncommon than DT/Cummins, but not anywhere near rare in most areas. Expenses aside, they have been nearly universally said that they are very reliable - just expensive.
Allison transmissions are in nearly every bus on here. I think I've seen one or two builds with a manual or other brand transmission, everything else is allison.
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TRANSMISSION
Now to the thing that haunts me and keeps me up at night.
The AT545 transmission. It's by far the most common in buses, and despite it's limitations it's often paired with an otherwise high-spec bus and becomes the "weakest link" in the drivetrain. It has no locking torque converter or overdrive, which makes it seem less than ideal for mountains or long distance driving.
It's also the cheapest and, again, seemingly one of the most common on the builds I've seen here. Despite it's shortcomings, many users have had great luck with it, others not so much. From my ~month of researching it seems quite a few people have tackled mountains at high grades (6-8%) with the AT545 as well as made cross country trips - this is where I'm stuck at, because a lot of people back it up while others recommend literally anything else.
I've found countless perfect buses if the AT545 could be considered as an option, and you likely will too. You just have to figure out if it will be suitable and if it will match your preferred style of driving.
The most recommended two transmissions I've seen are both Allisons - the 3060 and 643. The 643 can be interchanged with the 545 with a little work (IIRC DevRandom bus has a post about this, I'll try to find it).
Both have overdrive and a locking torque converter, which is much better for mountains and especially for long distance driving.
These are likely found coupled with the CAT 3126 and in many of the Rear Engine buses, 12/14 of the rear engine buses I've went to see have had a not-545 in them. The other 2 were shorter models with cummins and 545.
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CHASSIS
The conventional/Dog Nose are going to be front engine, the Transits will have either option.
I've seen a few claim that conventional are safer simply because the driver is placed behind the engine and you have a wreck "buffer" zone between yourself and the other vehicle. Possibly speculation, but I'm certainly not going to rule out transit models because of that.
Transits are wonderful for views. Having getting to ride in a few for test drives, conventional doesn't hold anything to the transit when you're looking for good views while driving. Also seems to make it easier to drive, even with a 40'er since you have a lot of visibility and no hood.
On the other hand, transits puts the driver ahead of the front wheels. Aside from getting used to steering, you have to take into account physics. You're going to feel bumps a LOT more in transits (unless it's air ride equipped) since you're ahead of the front wheels. Similar to sitting at the very back of a bus going over bumps - the chassis may only rise, say, 1 inch over the wheel wells over a bump, but a point further away from the fulcrum will rise, say, 2". You're riding on a giant level basically - the closer to the fulcrum point you are, the less you'll "feel" the road.
So, rear or front engine?
Rear engines are "pushers", and seem to come highly recommended. Not in a way to discourage people from choosing other options but more of just a consideration. Not everyone wants a high powered bus, being a 16 ton vehicle and all you may not want to be able to go 70mph and climb 9% grades at 60mph.
Front engines on the other hand are apparently easier to turn and navigate, however I can't personally vouch for this since the only bus type I didn't get to test drive was a front engine transit.
Rear engines have the benefit of not taking up space between the front and rear axles with a driveshaft. Engines > transmission > rear axle. Front engines you'll have to work around the driveshaft, since every bus I've seen is rear wheel drive. I mean, front wheel drive on a 16 ton bus? That's silly.
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BUYING
There is a thread here I've
been using, but honestly a lot of those links are dead. Here is a revised version with a few more locations and the dead links removed.
http://midwesttransit.com/
http://www.bargainbusnews.com/
http://ncschoolbussales.dpi.state.nc.us/
http://www.carolinabussales.com/school/
https://busmartinc.com/buses/
http://motors.shop.ebay.com/Buses-/6...%2C6000&_rdc=1
http://www.craigslist.org
https://www.creativebussales.com/
http://www.buswest.com
http://www.centralstatesbus.com/
http://www.taylorbus.com/buses/
http://www.nwbus.com/
http://www.a-zbus.com/
http://www.publicsurplus.com/sms/bro...aucs?catid=402
http://www.governmentauctions.org/la...us%20buses.asp
http://www.422sales.com/schedule.htm
http://www.kerlinbus.com
http://www.westernbus.com/
http://www.ks-bus.com
https://www.brandywine-eqp.com
https://www.busesforsale.com
Linear Mode
