88 Yamaha 200 2 Stroke Charging Problem--Please Help!

I have an 88 Yamaha 200hp 2 stroke with a charging issue. Dual batteries. Both are known to be good. I have a strong automotive repair background, but don't know a lot about outboards specifically.

Over the course of several hours of low speed (1000 RPM) trolling, it gradually kills a battery. I checked the voltage at the battery terminals with a voltmeter and it shows 12.25v at idle. At 2000+ RPM it increases to around 12.75v. I was expecting something closer to 13.5v+. I've been over all the wiring and connections and everything seems clean and tight.

A took a chance and disconnected 6 wires coming off the stator. I assume it contains 3 coils. (3 pairs of wires) Using an ohmmeter, I found the resistance to be the same on each pair and none of the pairs have continuity to each other. I didn't look at the stator any further. I didn't seem like a likely culprit, but it was an easy test to perform.

I found the rectifier assembly. Are there diodes inside this assembly? Any simple way to test it with a volt meter? Do these go bad frequently?

Any thoughts on what my next step should be?

There is a fuse between the reg/rect and the 12v junction. That motor doesn't have very good output at that rpm if you have much load by the way. What does the voltage do after running a while? If the battery is seriously discharged you would still have a modest voltage at your battery even cruising until the state of charge comes back up. That could take at least a half hour I would think.