Sounds like one of your problems is a lack of proper ground. The powerhead is at negative-ground via the black battery cable, connected right to the side of the block. But, the upper cowling, front and rear cowling supports, and lower cowling are rubber-mounted for vibration reduction. So, they have to have their own ground straps, which screw to the mid-section (behind the "horse collar" trim piece underneath the lower cowling), and also screw up into the lower cowling.
These ground straps are pretty thick Belden Braid-type construction and they'll pass quite a bit of current. If you don't have those straps in place, you need to find or make some. 2 per side and the bottom lugs use the screws which fasten the aluminum retainers for the rubber seal under the horse collar.
You may also find a 2nd black ground wire which connects to the lower cowling near the control harness plug. I can't recall if that year 100hp has one of those. If it does, you might need to undo the bolt and clean up the connections.
With the lower cowl grounded to the mid-section, you'll get a ground path thru the powerhead, thru the mid, thru the lower cowl, to the cowl supports and upper cowl. Which means your choke solenoid will work without having to connect a ground strap to the front cowl support.
Your engine may also have used some black ground straps the same size as the battery cables. There would have been (2) of them, one per side, attached to the upper-cowl-to-front-cowl-support bolt(s).
All these ground straps make up the "ground plane". If you don't have that, as you've seen your electric stuff like the choke won't work at all.
It's possible that the grounding issue is the reason for the lack of charging, but it also could be coincidental and you might find that your rectifier is bad anyway.
I've attached a rectifier test procedure, maybe that'll help.
If the rectifier is shot, you can upgrade to a more modern rect. very cheaply, a full-wave bridge rectifier with a metal case can be found on eBay for less than $5:
http://www.ebay.com/itm/281275599199
Just find a suitable metal mounting spot (maybe the front cowl support, eh? Then run the red wire to (+), run the (2) yellow wires to the "AC" terminals, and run a new black ground wire to suitable ground. A handy place to connect the ground is the mounting screw for the new rectifier.
Or, you can go with a factory rectifier, they're not extremely expensive. Check here at the iBoats store for those.
Part numbers to look up include 18-5707 (aftermarket Sierra Marine), and 816770T (OEM Merc part #). You'll still have to come up with a mounting point for the newer-style rectifier. But it does have screw terminals that your existing battery and stator wires will fit without modification.
Here's a typical example of one of the heavy-duty ground cables used on the cowling mounts:
http://www.ebay.com/itm/161077001688
And if you want to make some of your own lower cowl ground straps, Belden Braid is used on slot cars (or at least it used to be years ago!) and you may find it at your local hobby shop (also check eBay).
Hope that helps..........ed
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