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We have a 1990 3-cabin so have the same battery box,etc. you have. Here is what I did embedded in your questions below:

1. What batteries to use? I am leaning toward golf cart batteries. Their cost-performance profile is attractive. I am thinking I might as well get the biggest amp size I can as this will provide more power, limit the degree of discharge and extend their life. My battery compartment is about 12" deep from the base to the bottom of the cover plate. Will T-145's fit?

Response: I'm a big fan of golf cart batteries due to their durability and low cost over the past 15 years. Your box (if it's the same as ours) can accomodate 4 Trojan T-105 or T-125 without modification. I did have to add some wooden battens to keep them from sliding around and also built a hold-down system if worse comes to worse. The 105s and 125s are the same size - the 125s cost a little more but had more capacity. I think I had to cut off the threaded studs on top of the batteries to get them to fit the height and use standard older style auto clamps with threaded connections.

2. Alternator. Sounds like the original to me. From what I have read, it is a common upgrade.

Response: A higher output alternator is good and it should be Externally Regulated with a 'smart' regulator (Zantrex, Balmar, etc). I had a local auto electric shop build up a 120 amp unit for about $120. I don't know if it's as good as a Balmar but on our previous boat one ran 10 years and this one is entering it's 6th year without problems. Since I can buy about 4 or 5 of these for the cost of 1 Balmar that's the way I went.

3. The pro-mariner charger. I would guess original. Seems to work adequately and is capable of charging 3 banks of batteries. Is this a "smart-charger which will sense charge and just provide conditioning current after full charge is accomplished?

Response: I don't know about the Pro Mariner but a smart charger is a good thing. It almost eliminates battery maintenance - I add water once a year and could probably to 2 years with a Power Stat 20 amp.

4. We have a small inverter to power the T.V. Not sure we need more than that for cruising the Bay.

5. We have the original bank 1 and 2 voltage gauges on the panel. Are there better gauges to indicate the capacity of the battery? This would be fine for the start battery, but the house side would benefit by a more sensitive means to assess usage and capacity.

Response: We have the separate cranking battery you describe also and combine all 4 golf carts into a single house bank using the original 1-2-ALL-OFF switch. We have a second alternator to charge the house bank and use the original to charge the starting battery so the 2 circuits are fully isolated. It's a bit complicated and required a custom alternator mount. Almost as good would be to install a battery isolator to charge the cranking battery whenever the engine is running or hooked to shore power. Since we treat the 4 batteries as a single house bank we use a Link 10 monitor on the house bank only. For the cranking battery a simple voltage meter is enough.

Of the many wonderful threads on this topic over the years is one started by Oscar of the Lady Kay on 11/27/04. After re-reading this and many others I've saved, I offer the following thoughts on a crude plan.

1. Upgrade the alternator. To which one?

2. Separate the start battery from the house on the discharge side. Either dedicate the old Hitachi to it and separate it from the charger completely or use a "separator" to allow charging from the alternator and charger to charge both house and start battery, but not allow the house access on the discharge side. Some have put a switched connection between house and start to use as a "jumper" in case the start fails. The combiner plan sounds better to me than 2 alternators.

Response: As noted above the 2 alternators are nice since it gives redundancy. The cost is in the special mount and a separate sheave on the crankshaft. The battery isolator (the solenoid, not the diode type) gives you most of what you are looking for. Some have a manual override to act as the jumper you describe.

3. Have the battery switch use position 1 as left house bank and 2 as right. Keep in all position to spread out discharge to extend life.

Response: True. But don't include the cranking battery.

4. Use golf cart batteries. Get the biggest ones that will fit. T-145's??

5. Obtain a better method for assessing house side discharge.

Response: The Link 10 works very well. This is our second boat with one and I am completely satisfied.

Our second alternator puts out 125 amps cold. It will drop to about 115 once it warms up but the regulator kicks in a and starts to limit the amps as the battery voltage rises. Even with the batteries drawn down below 50% the alternator puts out less than 80 amps after about 10-15 minutes running.

You can get significant charging performance with an external regulator. It's a fairly involved topic but internal, automotive regulators only maintain a 'float' voltage indefinitely. The external, multi-stage regulators go to a higher voltage until the batteries are nearly fully charged then cut back to the float voltage.

The stock alternator can be converted to external regulation without too much difficulty. Any good auto electric shop can do it or you can do it yourself. I have a write-up from Heart Interface I can email to you if you are interested.

Working the alternator harder means you need to take good care of the drive belt. Buy high quality ones (Gates, etc.), keep them tight and replace them often.

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Looking at the manuals they look exactly the same. I expect one company builds them and labels them for the other. They are 'P' type which is what most externally regulated altnernators require. The Xantrex manual is a little more clear in how to install to any alternator while the Balrmar manual is more greared to a plug-in connection to their alternators. Both manuals are available on-line.

If your stock alternator were converted to external you can use either.

I don't have a combiner since the systems are isolated. When at the dock the cranking battery isn't charged but since there is no load on it there's no need. I did install a heavy duty switch to jump the 2 systems together in case I did end up with a flat cranking battery or if there was a problem with the auxilliary alternator. Then the stock unit could charge the house bank along with the cranking battery.

I have complete drawings of the mount and the sheave created in Autocad. I'd have to check back with the machine shop that made mine to get an updated price. There are multiple groove sheaves available for the Yanmar but I wanted a larger diameter and I got mine made for a little less money as I recall. This one bolts right on the stock engine sheave. Ballpark for a mount and sheave is about $300, maybe less. If there was enough interest I could have several made up and get the price down a bit. Maybe even include an alternator in the package.