Well, here's what I learned from the gentleman at Weitzel's D.C. Electric in Norwalk, Ohio.
The big round capaciter was used on the first years of the 12SI and also in the previous 10SI models. The later 12 SIs got a small black rectangular capacitor that tucks under the rectifier's negative side on the right. (I presume the change was for better heat dissapation or manufacturing costs.) They do the same thing.
Resistor from Trio to Ground
These are to help trip the idiot light. Of course the SJ's that got the 12SI alternators don't have said lights. Instead they have the ammeter and a resistor. So those 40 ohm resistors aren't needed in our Waggys, and that's why they're not in original alternators or in parts book.
I'm going to spend some time looking for voltage drops, loose connections and grounds. Then go back to getting some more juice out of the alternator. I also confirmed that the only things needed to upgrade to a 94 amp alternator is the stator and a higher amp rectifier (identified by the curved fins). I think this assumes that the rotor is really a 12SI rotor not a 10SI rotor swapped in during remanufacuring. That's harder to spot.
Props to Mr Weitzel or whomever answered the phone. I called there because someone suggested his e-bay store
as a source of parts and a little poking around with google showed it was a real repair shop. So he also has a lot more inventory than ebay shows