We have fuel to the rails, power to the injectors, but no Pulse?

We did a motor swap. It is a 5.3L, the new engine has only 1,200 miles on it and is out of a 2002 Avalanche. Should have been a plug and play. We have done several similar motor swaps for other people and they turned out great. We are not getting so lucky with ours. We have been throught the VATS relearn procedure twice. The first time with the avalance computer. It seemed to relearn it successfully, no security codes with either computer now. We started off with the avalanche wiring harness, when it would not start, we changed it back to the original wiring harness. We now have the original wiring harness and computer back in the truck. We have fuel to the rails, power to the injectors, but no pulse. We have been fighting this for a few days now, and nothing works. The only sensor that has not been changed back to the original one, is the cam sensor. The motor that came out of the truck actually still ran like a champ. We decided to do this because the original motor and transmission had 175,000 miles on them and we had bought the motor about 3 years ago, and just recently had a transmission rebuilt for the one that was starting to have some minor issues. This was a perfectly running truck when we parked it in the shop last weekend and started this project. We are at our wits end trying to figure out what is wrong.