It's one thing to look for and buy a bus with a preferred drivetrain, such as the 8.3 Cummins (or whatever), but what if you want a drivetrain that was never offered in a school bus to begin with? As an example, an ISX Cummins or 425 Cat? In this case it might make more sense, if you are absolutely determined to have one of these drivetrains, to buy a bus with a dead or missing engine for practically nothing and begin your swap there. Just buy one that meets whatever other criteria you have in terms of length, headroom, brakes (air or hydraulic), air ride suspension, etc. You could even move up to a newer model past '04 as long as you are informed about all the emissions hardware that will be removed and not used on the replacement engine ... the engine/vehicle computer won't be happy about that. In which case it would make sense to either find an older bus without one, or plan to swap to independent gauges if needed to eliminate the vehicle computer.
Also, as appropriate, don't forget about the clutch pedal if you'll need one. And that AT545 won't last long behind a big motor.