OK one more question, but it's still related for the most part. Hope you don't mind!
My alternator is a 90 amp Balmar with ARS-5 external regulator. I don't know what gauge the charging wire is currently. Regardless, what should it be for a 5 foot run to the house bank?
You actually have a 10 foot run, there and back. Remember all DC circuits are a loop. There should be a negative wire that is a minimum of 4ga and a positive wire that is 4ga. This will still result in a 2% voltage drop or 0.3V drop @90A. So at 14.6 you'd be seeing about 14.3v at the battery. 2ga would be better than 4ga.
In either case the alternator should be grounded direct to the house bank, or a closely located buss, for best performance. It should not just be connected to the engine ground then back to the bank. Most Balmar's are isolated ground not case grounded. This will help reduce any more VD than is absolutely necessary. Both of these wires, neg & pos, should be led to the house bank for the best performance.
Above all else your ARD-5 regulator should sense the house batteries not the alternator but this needs to be done with care and wired properly. This will eliminate any VD issues as the regulator will compensate the voltage. You'll still have VD in the wire but the banks won't see it because the regulator will compensate for it.
So how do I size the alternator wire? I know the fuse will be MRBF and I'll size it according to the alternator wire size.
You can size it lower than the wire size and still be fine. The fuse should be as close to the batteries as possible. We are trying to get as little VD as possible and that requires large wires. With battery sensing you can get away with smaller wires but bigger is still almost always better.