(Added 01/03/2011) Turns out this was the case. I modified the battery mount support bar so it did not rest on the motor bracket and that helped. I also put the firewall pad and insulation back in the car. Makes it look more like a car and less like a go-cart.
The car is running great. My commute to work is 22.5 miles and 22.5 back.
I used 40.8Ah to get there averaging 1.81 Ah/mile (freeway speeds 60-70 mph). I used 61Ah to get home including a 4.1 mile lunchtime trip to staples for supplies. This works out to be an average of 2.25 Ah/mile. This is interesting. My trip home was in the dark so I needed the headlights. Also my headlights are pop up creating more drag? Not sure why the increased Ah difference. Possible elevation changes (ie downhill to work uphill home).