So, a few updates on it. I toasted the trans ECU, sent it off to Transmission Instruments who fixed it beautifully for me and replaced the panel and screen which were in poor condition. Shifts great now.
Tried an electric/hydraulic, couldn't get the flow I was hoping for. 2 GPM was the only affordable system an its just not fast enough. To get more hydraulic power I see a few options, either find a way to get a clutch pump under the hood which is very space limited, piggyback a second electric pump in parallel, which would be clumsy and still power limited, but cheap and easy, install a front shaft PTO, or get the PTO to run while in gear.
From my research, the PTOs on these trucks are not the hot-shift types, which require a clutch pack so they can be activated while running. These are a lot more expensive, but honestly not that much more than a clutch pump would be. 1500 new and 1000 used or so. I have read about people having army trucks with these on them, but haven't talked to anyone with actual experience or knowledge about the install. I'm thinking I'll call an Allison dealer tomorrow and see if they have any insight?
Other than this, the project is coming along pretty well. Having to do some fiddling with the hydraulics because with 3 separate valve bodies I have to close 2 of them off whenever I run the 3rd so the bypasses don't allow fluid to cycle. Oddly enough, even with my third block, both of the original blocks seem to have open centers and if I deadhead an outrigger to close off the lower block the crane will run about twice as fast. I'm thinking I'll use the integrated shutoff solenoid to the top block to shut it down when I use my auxillary block and use a ball valve to keep the lower block off since its rarely used anyway with mast and outriggers on it. I got a 16 channel remote control relay block to turn everything into remotely controlled which has been awesome.
Still battling the hard start but will try turning fuel up. Part of my issue is there is just no crank power in the batteries. 10 seconds is maybe all you get. I took them off and fully charged them and they tested ok on my load meter but somehow they must be bad. Some of the grounds will get hot enough to burn you in only 10 seconds of cranking, which doesn't say good things about the cabling but shouldn't totally drain your crank power I wouldn't think.