The FIPL (Fuel Injection Pump Lever) also called the TPS by most auto parts stores, is only there to tell the TECA (E4OD Transmission Controller) where the throttle lever is. The FIPL has no control what so ever on the engine or starting. If it is not adjusted correctly, it WILL cause shifting issues with the transmssion. Since you were in the area of the IP working, make sure all the electrical connections are made, and correct.
Also, did you remove the IP to do the head work. I am sure you did, so if you did, how did you remove the IP? Did you remove the plate below the oil fill and remove the 3 small bolts, and then removed the IP from the gear tower, or did you remove the IP, Gear Tower, gear and all as one unit. If so your issue may very well be timing.......
Also, please add your truck information to your signature so we all know what you are working on. To add this information, click the User CP link and then click Edit Signature.