Diesels are very finicky about having enough voltage/current to start - If the starter is good it sounds like maybe you're not getting enough current to it to turn the engine over fast enough to start. I'd double and triple check all the connections (pos. AND neg.) to make sure they're clean and tight, and also check the condition of the cables themselves. It's not uncommon for cables to corrode inside the insulation (and look 100% fine from the outside.)
P.S. I'm jealous of this project.
My last diesel was a joke when it came to cables and connections. I thought that might be the case here also. I only double checked, not triple. I am buying fresh batteries before I dig further.
I charged the batteries over night, and still had slow crank. I only cranked for a short bit. When I put the battery back into my other truck, it was so dead it wouldn't start the gas engine. I take this to mean one of two things.. 1- the starter is drawing waaay too many amps and killed the battery quick, or 2- that particular battery might not have had a good connection... except it did read on my volt meter as getting charged..