Well, after some initial testing I briefly disconnected a controller from power and upon reconnection had a huge spark on the terminals.
The following describes in order what happened next.
1. The controller stopped working
2. I did some testing trying to figure it out, (disconnecting, reconnecting, check for power etc)
3. Realized I heard a click every time I connected the ignition wire??
4. Realized working controller has no such click????
5. Realized the controller was solid state and had nothing inside that could click?????????
6. Thought (spark jumping inside case is the click???)
7. Took controller out of casing to inspect
8. Connected power
9. BANG!!!!!!!!!!!!!!!!!!

10. Dropped control board
11. Flames shooting across surface of control board!
12. Disconnected power

FLAMES!!!!!!!!!
OOPS!
I guess the spark was grounding itself through the case


It's worth noting that there is another possible cause to this problem. I had decided to experiment with the anti theft motor lock setting on the controller which had resulted in some smoke just previously to disconnecting and reconnecting power, this was done to re-program the controller. Considering one of the 4110 fets is blown to bits I'm wondering if the problem was actually the fet being toast before I ever reconnected and got that spark. When I had the motor lock set high I had brief heating of wires and smoke.
Any suggestions on what components I should replace on the controller? Besides the obvious failures of one fet and a capacitor?