Looking damn good!!
I'm really looking forward to your progress on the truck and trailer since we both have similar setups with similar goals for them.
You're on the right track with running wire up to the alternator instead of messing with the converter in the trailer. The converter puts out 30 amps per circuit at best and they are notoriously low quality. They're also not great at charging batteries, especially AGMs, so an intellicharger or something would be nice for when you're at your shop.
The fact that you don't seem to be getting any appreciable charging from your truck bothers me. Have checked the plug with meter to see if it's putting out voltage? You did take the relay in the plastic bag in your glove box and put it in the fuse box under the hood? For some reason Ford doesn't install it at the factory or dealership and your truck won't charge the trailer without it. That only gets you 15 or so amps, but it will certainly help when you're running down the road and not connected through the quick connects (I'm assuming you won't keep them hooked up while you are towing down the road).
Hopefully that helps. Keep up the good work.