Johnny Dearborn,
You mentioned a few things and did not mention a few other things that leave me to believe your setup is the cause of your problem.
1) With two 12 volt batteries in parallel, for them to work right, or better stated "as right as possible", they must be butted up against each other with short fat ~8" cables tying them together. Thick buss bars would be better yet, but very few people would do that. Long cables in between 12 volt batteries is ripe for failure.
2) The batteries MUST be of the same technology. You cannot mix a wet cell with an AGM and get acceptable performance...even if butted up together with thick buss bars. This is because the AGM requires a different charging voltage and charging behavior. That is why chargers have different settings for the various technologies.
3) Even batteries of the same technology, mismatched batteries in brand, capacity, and even age, the weaker battery will bring down the performance of the better battery. Two brand new identical batteries with the same production date vary enough to develop performance issues starting in the 2nd or 3rd year.
In your particular situation with the two batteries separated with a length of cable as you have described, you would be so much happier with two 6 volts batteries because the cable length will not adversely affect them nearly as much (or not at all) as with 12 volt batteries.
If you decide to go with 6 volt batteries, wet acid or otherwise, I personally like to buy mine at Sam's Club. Go on their website and see for yourself.
Your 3 year old on-board charger must be configured to the technology of your choice. Read through the owner's manual before selecting your technology. That charger might not support certain technologies.
BTW, I like the idea of the battery box venting to the outside.
Good luck!
Ron Dittmer