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