There are a large (50 amp?) alternator output and small (5-10 amp) voltage regulator fuses in the fuse box

i'd check the output at the alternator output terminal first
you should have charge outout there... then probe through the charge wire going to the battery and see if there are any high resistance spots or if it has fuse links anywhere check those.

some of the C & P cat trucks had similar issues...
alternators would test good but still wouldn't charge at the battery and i found many times the fuse links were bad or had bad connections. Also if it has an emergency disconnect switch check that, the charge circuit probably goes through that too.

oh yeah... make sure you have a good ground from engine to frame... no ground might mean no charging.
Just a thought or two ;o)

good luck

If you have verified that you have voltage at all 3 inputs to the alternator connector and they are 2 at battery voltage and one at about 90%. Have verified you have a good ground to the housing?

I'm with Jeremy S on this. Check the wire to the starter. If it doesn't have one, run 1.

I had issues with bad ground wires and bad batteries. Good luck

what is the voltage at the output wire of the alternator? if it is good, which it should be since alternator checked good, run a wire to starter positive terminal or battery positive terminal. This is based on the assumption that regulator voltages at alternator terminals are correct.