If the choice is between an older bus with the DT360/AT540 or a newer bus with the DT466/2000 I would not hesitate with the newer bus.
The DT360 is a great little engine. Think in terms of the lower HP version of the Cummins 5.9L/ISB. At the most it is going to be rated at 210 HP and could be as low as 160 HP with the most common being 180 HP. In a small bus with the AT540 transmission everywhere you go on the highway will be foot to the floor and slowing down for any hill.
The DT466E in the newer bus will have much more torque even if the HP ratings are the same. What that means is it will not slow down as much on the hills and with the 2000 series transmission you won't have to bury the throttle to maintain 60 MPH.
I would assume if the newer bus has coach A/C it also most likely has tinted windows. On a hot day tinted windows in a school bus can make more than 20* difference in temperature between identical buses with one having tinted and the other having non-tinted glass.
I realize your goal for your bus is not a full on camper or tiny home but installing some of the amenities is still not a bad idea. Having your own private toilet can be a luxury that is beyond price at times. Think of hot summer afternoons with the only "facility" a portable toilet that hasn't been serviced recently. Having your own private "facility", even if it is only a portable or composting toilet is well worth the effort at that point. And having a sink to clean up after using the "facility" is a much preferred option to just using hand sanitizer.
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A fridge to keep your drinks cool and a microwave to heat up your leftovers is one of the really nice advantages of an RV over driving just a car across the country.
I think perhaps you are overthinking some of the RV requirements.
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Build one cabinet with a counter top on top of which you could have your sink with a space for your stove. While traveling and not in use they could be stowed under the counter. The end of the cabinet could hold the fridge and microwave. Over one of the wheel wells you could build a frame to hold the toilet. When not in use the portable wall could be stowed out of the way. The whole thing could be done in a cabinet not more than 8' long and done in a way that would not block the windows. Or not block very many of them very much.
There are a lot of people who have done very minimalist conversions. Some from their desire to be minimalistic, some from their lack of $$$$, some from lack of skills, and some from a desire to take the bus out and find out what works before spending a lot of time, $$$, and effort building a full on conversion.