Just a thought, sometimes our charge systems don't like mixing wet/flooded with gel/AGM batteries or different vintages. Is your starter an AGM too? or a little older?
2003 Ford E-350 SMB RB-50
7.3L w/DP tuner & 4" exhaust
Quigley 4X4 (heavily modified)
CCV high profile insulated pop top
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'03 Ford E350 7.3L Diesel
(de)SMB'd Custom RB-50
Quigley 4X4 w/Deavers & Agile Offroad's R.I.P. package
CCV High Profile Pop Top
DerPo...can you post a picture of your separator/isolator?
The simplest test to determine if the separator is functional is to just take it out of the circuit......just disconnect the battery cables from each battery bank from the separator and connect these directly together. Buy a 50 cent nut and bolt and fasten them together....
With the engine running you should see around 13.5-14V at both batteries.
Once you are convinced you have a separator/isolator problem you need to figure out if you have a separator or an isolator. An isolator is usually a finned aluminum box with two battery terminals.
Rally asked if it was a blue thing.......is it blue?
If bypassing your separator/isolator does not result in 13.5-14V at the house battery, you have another issue, like a fuse/circuit breaker etc.
When checking the voltages, be sure that you are disconnected from shore power. If you are not seeing over 13V at the house battery when plugged into shore power (assuming that you have a converter or inverter/converter) that's a different issue.
Everyone I'm so sorry for wasting all your time and effort.
While all the connections were tight, there was one smaller red wire that managed to sneak under the battery while I was installing it. This Came to me this AM at 0100 as I was listing to the rain racking my brain over this.
So problem solved! Thanks for all the input, and at least now I know where the separator is under my hood.