The LBZ is pretty user friendly. The LB7 has problematic injectors, the LLY has some cooling issues and the LMM has more emissions crap. IIRC, the later LLY's didn't have the cooling issues and were basically an LBZ with an LLY tune, these rigs were the ones available with the 6ap Allison. Also IIRC, the LMM has the same tune as the LBZ but has the additional emissions crap holding it back a bit.
The 6ap is way easier to mod in terms of a shift kit for a basic tune than the 5sp is, and I feel like is indefinitely better to drive than a 5sp, so I'd look for a rig that has the 6sp regardless. The LBZ has the best stock set up regarding tune and power of the group and no "significant" issues or problems to work around. It's easier to replace the injectors, and arguably makes the best power with the stock set up and even when tuning for the stock engine. The LBZ's greatest bane is it's pistons when you start to turn up the power past the realm of 550whp. (Ask me how I know)
So IMHO, a late LLY or an LBZ would be your best bet:hug: