sounds like a cool package with lots of options,
check the diesel forums to see what can be done to turn up the injection pump/governor,
look at a 2 speed rear axle out of a medium duty truck to split your axle ratios,
which allison trans, the 545's are non lockup, the 643 lockup in 3 & 4,
your bellhousing should be a round opening standard SAE size, that will interchange with most compatable engine and trans packages, just make sure that the trans is rated for the torque and hp of the intended engine.
look for a takeout engine & trans package that was factory matched for compatability,
keep us posted