Alright, update time. I checked the circuit this past weekend. I found no problems. So, I tried the circuit again and it seems to be working perfectly again... I have no idea why it acted up again.
So, I have been using it all this week and it's been great. Last night for example, I got home from work and plugged in. My wife and I had a meeting to go to and left about 30 minutes later. The charger was already done charging. That's a nice indication.
This meeting was about a 35 minute drive there and 35 minutes back. The entire trip we had the heat going and headlights on. This was pulling about 20-25A from the battery. The battery is about 80Ah, and it was around freezing temperatures. As we kept going, I made sure to use regen as much as I could to keep it as charged as possible. The voltage started out at about 12.2V and slowly dropped until it was roughly 11.1V when we got home.
What I really found interesting was how regeneration acted as the battery became more and more discharged. Usually, on my trip to work I engage the alternator and it jumps to 60A or so and quickly tapers off to some lower number. Last night on the way home as soon as I would engage the alternator it would peg at ~80A and stay there. As the trip went on, I noticed it would jump to 80A, but the max voltage was lower and lower. Towards the end of the trip I was only a little over 13V while still charging at 80A. This makes sense of course, but it is a new observation for me.
So it seems that on my daily commute I don't use enough battery capacity to get the battery out of the constant voltage mode of charging and into the constant current mode. Unfortunately this limits the power I can get out of the regen setup. On the plus side, my battery is definitely large enough and lasts longer than I thought it would, especially in the cold.