How many Trojans? 6 or 12 volt? Are you going to try that marine charger from Pro Charging Systems or stick with your current isolator?
I kept the battery separator in place, for a couple of reasons. One, if the Dual Pro On-The-Run charger doesn't work out for some reason, it's a snap to go back to the previous setup.
Two, it was quicker and easier to leave it in place. When the engine is running the battery separator engages and sends charging current to the battery bank. In this case, it sends the charging current to the Dual Pro charger, same as if the separator wasn't even there, the charger doesn't know the difference.
The cable from the battery separator goes back to the house bank and connects to a Class-T fuse block, and then another cable from the fuse block to the main positive bus bar. I replaced that second cable with the Dual Pro charger, connecting it to the fuse block and then to the bus bar. So the alternator feeds the charger (via the fuse) and the charger charges the batteries.
The second cable that connected the fuse block to the bus bar, I'll carry that with me just in case the charger goes goofy, and I can then quickly go back to the way things were before. In the pictures above, it's the red battery cable on the far left side that goes from the fuse block and then up to the bus bar on the rear of the bunk. I simply replaced that segment with the charger.
The batteries are
Trojan J305E-AC 6-volt batteries, 305 amp hours each.
As a comparison to the popular Trojan T-105 (Golf Cart) batteries, the J305's (Aerial Work Platform) are about 2 inches longer, about the same width, but about
4 inches taller. And 20 pounds heavier. The next step up from the J series would be the L16 series (Floor Scrubber) batteries.
T-105
Amp hours - 225
RC @ 25 Amp - 447 minutes
Weight - 62 lbs
J-305E
Amp hours - 305
RC @ 25 Amp - 645 minutes
Weight - 83 lbs
The four 6-volt batteries are connected in serial pairs, and then in parallel, for one large 12-volt battery bank with 610 amp hours capacity.
Golf cart and other Trojan distributors have these for around $250 a piece. Online you can find them at $220 (plus LTL shipping).
One place online is $185, where I got mine,
Staab Battery, at the main location in Hazelwood, MO (St Louis), but they have locations in Springfield and Aurora, IL (will not have the J305's in stock at the other locations, but can get them in 2-3 days when the normal truck run from St Louis takes place). If you pick them up in person at the main Hazelwood location, they'll probably give you a decent price break. They certainly did for me.
Even without a price break, they're the cheapest I know of. I got mine for $160 a pop, for four, with core exchange of course.
Staab Battery is a manufacturing shop buried back in an industrial area behind a steel pipe plant where they don't have many retail walk-ins (that's for sure). When you see the place, it looks like the results of, "I know a guy who knows a guy," kind of thing. They're a distributor and manufacturer of batteries, and they rebuild batteries there and do industrial deliveries. So it's a working place rather than a retail shop. But no overhead means a better deal, and the guys in the shop are pretty kewl.