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Just a couple of things to consider-
1. Did you remember to polarize the generator after it was unhooked?
2. A generator doesn't put out current at idle speed. Run the engine about 1500 rpms and check with the multimeter.
I just use a continuity tester but a multimeter should work.
With the battery connected, engine off - disconnect the wire from the field terminal of the regulator and momentarily touch the field wire to the battery terminal of the regulator. Normally you'll see a small blue spark. Reconnect the field wire to the field terminal.
I know it sounds too simple, but if you don't do this when you have the electricals apart the gennie may not charge. 12 or 6V doesn't matter.
There is a 2 page explanation in the shop manual on how to check the output of gen and reg with a volt meter.