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Did you run the self test, see if the computer can tell you anything.
Pull the spout jumper out, test see if it fires the injectors without it in place.
If no help test/check the TPS. Back probe the connector, test ground and signal wires, should read 0.50 to 1.0V key on engine not running with the throttle plate fully closed, if you get 4.0 to 5.0volts for some reason, say the TPS installed incorrectly for example, that's likely going to be the problem.
Thanks for the suggestions. Boss said I can pull it back into the shop this evening after close and work on it, so I will be double checking the orange ground as well as running through your ideas. I will let you know what happens.
Ok, so I got the truck back in the shop. Tried to do a self test and could not get the check engine light to blink, so that was giving me a hunch that my grounds might be screwed. The PCM worked fine before I did the engine swap so I thought it very unlikely that it was on the fritz. So I looked up the EEC-IV connector pinout at Ford Fuel Injection and tested continuity at the four ground locations. I only had continuity at one of them. Doh. I then proceeded to fix that problem and it fired right up. Now I just have some little things to do and it will be ready to rock.