Thanks for the great input - I admit some of these are "leading questions" for the group.
Brian yes, the stock Hitachi 35A alternator had an internal regulator. Since the little one-lung Yanmar can't spin a larger alternator, I bought a second 35A Hitachi and had it rebuilt with the field wire outside the case, then installed an ARS-5 regulator. Maybe it's ramping down too quickly. It drops from 30A to around 12-15A after a few minutes and down to 7-8A after a few more minutes. (@Skip - yes, I carry the stock alternator as a backup both for the alternator and the external regulator.)
Slack, I've been looking at that Victron monitor - Fisher Panda (I think) is selling a bunch of them off via E-Bay at $148. Like most of the other "two bank" monitors, Victron's two-bank version just measures voltage on the second battery. Do I need two of them for full data on each battery? I still have the shunt from the Link 20 - fancy thing and heavy, but maybe I could use that the way Brian suggests. I get system voltage through my ST-60's so I really just want to measure amps in (to verify the solar panels are working) and amps out (to monitor usage). An installed in-line ammeter would do it. I suppose those come with their own shunt? Where would you install it?
Here's another issue. For better weight distribution I moved my batteries forward. This required about 10' longer battery cables. Now I'm seeing about a .3 -.4 voltage drop at the instruments and autopilot. Do I need to worry about this? If so, it means a second switch/fuse panel up near the batteries, and I don't really want to do that.
@Bob, you likely don't need to worry about the .3 to .4 volts drop at the instruments, they are designed to work over a very broad range, unless you see that much drop with only the instruments on and not charging with engine. If the drop exists with just instruments it means you have relatively high resistance in your power run from instuments to battery, and maybe other items are seeing that drop as well. If your alternator regulator is also seeing the drop, and it is likely it is, as it as far away from the batteries as anything, this could explain your regulator dropping off quickly while charging. If the autopilot is sharing some of these same feed wires you may have big drops momentarily as the AP battles the NW swell on your way to Hawaii. This could cause an AP shut down [on Red Sky the AP has a dedicated power run direct to batteries with a breaker next to drive motors]. You can also get some drop in breakers, I have seen as much as 0.2 volts across some older breakers. SSB transmission could also suffer as at 100W output the SSB will see spikes of 20 amps, if the voltage drops momentarily below about 11.8 volts the SSB will "FM"/distort, a big deal if you are using sail mail, and making for really lousy voice comm.
I would suggest you do a simple analysis. Put a load at the ends of your wiring runs, like at the AP power terminals, SSB terminals, etc. A simple load device is a 12 volt turn signal bulb. It should pull a couple amps. Now measure voltage at the lamp and at the battery. If you see big drops start working your way along the wiring checking breaker, all crimp connections, etc. If you see anything in the range of 0.1 volts drop across any connection point consider replacing and/or improving the connection/breaker, etc. Sometimes just cleaning and tightening will work. If you see a large drop of the entire path but the connections look good, start considering changing to a larger wire size.
Alternator: You added a standalone regulator ! Great ! Does it happen to have a pair of "sense" wires broken out ? They would be two small size wires connecting to the alternator output. If these exist you could disconnect from the alternator output and extend them all the way to the battery being charged, or the large power battery switch. This then allows the regulator to see the actual battery voltage and not suffer from the drops seen in the large wires going to the battery (known as a four wire measurement). THis is the best solution as it completely rules out drops due to high current and connections that can degrade with age and/or vibration.
You may be suffering from a poor connection somewhere. As current passes through while charging, it heats up and the voltage drop rises slowly over time. As the drop rises the alternator current falls. MY main perko switch did this. I finally noticed a large drop and the thing would get a bit warmish.
I hope this helps.
