Just got spending 2+ hours reading all 45 pages, holy crap what a story. I'm in the first stages of a build plan and picking a bus for myself, wife and 3 fur children to live in full time. You have so many inspiring ideas it's really great. I'm also happy to see that you had no major drive train issues after driving all those miles. The 3126 isn't one of cat's best engines, but with proper care they can last a long time.
By the way i've done a bit of work on the Cat 3126 before in a medium duty truck platform. If you are having starting, or low power issues on a 3126 one of the first things to check should be fuel pressure supply. The engine I worked on had a mechanical lift pump that supplies 50-60 psi to the injectors. The system is a bypass/return type system and the fuel pressure regulator is on the back of the cylinder head, right at the fitting that you replaced the leaking fuel line on. Blocked filters, worn lift pump, or defective fpr can cause low fuel pressure. Also there is a check valve in the lift pump that should maintain pressure even after engine is shut off. Long crank on first start up of the day usually means leaky check valve in the lift pump or reg bleeding off.
The truck I worked on was a single axle sewage pump truck that had starting issues that began at 86,000 miles and lasted until about 200k miles before they finally brought it to me to check out. Tested fuel pressure and it had about 20 psi. I would guess that it had low fuel pressure all along due to a stuck/malfunctioning fuel pressure regulator.
It had 1 reman cat injector installed before, and we ended up replacing the other 5 because they were weak from low fuel pressure. Power was greatly increased and it ran much more clean/crisp after that. It has a 6 Speed Eaton and the driver said he could pull a hill in 5th gear after the repairs; he had to gear down to 3rd before when loaded.
I would go as far as to say it would be a good idea to add a fuel pressure gauge because proper fuel pressure is critical to injector life on a HUEI engine.
I look forward to updates.