Update on Timing System....
I think I figured out what I was doing wrong with the timer. First, the timer runs with a constant input. Pulling the input stops the timer. I had assumed a input would start it and another input would stop the timer. The second is that the timer comes from the factory set for negative logic. The input is switched with a ground not a 12v positive. So, it looks like I'm back in business...
I do need to rewire the relays a little, but so far I see no problems.