Well, here is an update on my Low Rider. I pretty much took the whole bike apart looking for anything that could be a problem. I measured the resistance of every wire in the bike. Inspected the harness for chaffing. No problems found in the harness and all connections looked OK.
I pulled the intake off, cleaned it and replaced all of the seals, no change.
I bought the Harley fuel pressure adapter from Matco for my fuel pressure gauge. It is part number HPFA502 if anybody wants one. The fuel pressure the fuel pressure running was between 40 and 45psi. As soon as the engine was shut off the fuel pressure would drop to 0 instantly. So, I fugured there was either a problem with the regulator or check valve. I dissassembled the fuel tank. In the tank I found a couple of problems. The connector for the fuel pump had a bad connection and had started to burn the connector in the pump. The line from the pump to the regulator had started to crack where the nylon tube is pressed over the fittings. So I replaced the fuel pump, filter, in tank harness and fuel pump line to regulator, which the dealer said comes with the pump, but it doesn't. You would think this had to fixed the problem, but it didn't.
So, at this time I figure it has to be a problem in the ecm, iac, injector or something. I bought the Daytona twin scan to get an idea of what was going on in the ecm. When the engine would start to miss and back fire the iac would start to rapidly ossillate between full closed to about 20 to 25 steps out and would randomly jump to about 100 steps. The miss, back fire and stall is only at hot idle. When the bike is cold idling at 1000rpm the iac is about 35-40 steps. So, I removed the iac and connected it to my ohm meter. Cold it looks ok. I took my heat gun and started to heat it up and found that when it gets hot the position sensor starts to change resistance, which I think confuses the ecm.
I replaced the iac and have riden about 1000 miles with out a problem. There is a lot more that was done but these are the biggest problems I found.