I'm having a similar problem with my CUCV M1008. I recently re-sealed the bottom end. New rear main, oil pan, front main seals were all done. While I had the pan off I noticed the timing chain was pretty loose, so I replaced it and the harmonic balancer along with the water pump. When I was putting everything back together, I replaced the two alternators with some rebuilt ones from O'reilys, and paid about twice as much as having them rebuilt by a shop, but figured live and learn.
Anyway, when I was finally ready to crank her back up, the batteries were dead. So I put them both on some trickle chargers, and a day later they were charged. When I went to crank her up, she fired right up, ran for about 2 seconds and died. When I tried again, she turned over and over but would not crank. The batteries also died quickly, so I hooked another battery up as a jumper, and this time she fired up and ran very well. I could tell the difference the timing chain made since she used to pulsate a little @ idle, and now has a steady purr.
However, gen1 light was now on and would not go off. and gen2 light was very dimly lit. Usually, with the old generators, the lights would come on and stay on until I revved the engine slightly, then would go off. Also, the batteries were strong. I decided to R&R the alternators with the old ones. This put everything back to how they were before, but my batteries still are weak. Could it be since the timing chain puts the timing of the valves back to when the engine was new, it is now harder for the starter to turn her over? If this is so, should I get rebuilt starter?
Any advise from those with good electrical experience would be appreciated. I am a transmission mechanic of sorts, but not too strong in the electronics areas - I know enough there to be dangerous...