Ok so I just turned the key to the "on" position and jumped the starter with the starter relay out, truck fired right up. No theft light is on, so where do i go from here?
More info....
Key out while starter relay still in = engine turning
Key in and in the "on" postion and relay still in = no engine turn (nothing)
Key in and "on" while starter relay out = engine fires right up
So we know the engine will start and run.
We know PATS is working fine.
We know the ignition switch works, at least in the ON ("RUN") position.
At ignition switch, check for +12V on the R/LB (red w/ light blue stripe) wire when the key is in and the switch is held in the START position. If you've got that, move on.
That voltage has to get to the starter relay, but in order to do so, it has to through one or two places along the way.
If you have a manual gearbox, it goes through the CLUTCH TRIPLE FUNCTION SWITCH (clutch/starter interlock. In going through this switch, the wire color from the ignition switch is R/LB, but leaving the switch it is pink. Might need a friend to test it, but check for +12V on the pink wire while clutch is pushed in and key is held in START. If +12V is there, you can be fairly certain the problem is your starter relay (the only other parts in the circuit are wire and the socket the relay plugs into).
Automatic transmission rigs will have a jumper plug installed in the harness where the clutch switch would have been connected. On the automatic, check for +12V on the pink wire to verify that the jumper is doing its job. The next place to check on the automatic is the range sensor. If everything worked before the swap, it is unlikely that the range sensor randomly failed on the transmission - much more likely that the wiring to/from it would be a culprit. The connector may have gotten dislodged or damaged during the engine swap. The connector is on the side of the transmission, fairly close to the fuel filter. Probably has 8 pins, although it could have 11. Check the sensor for continuity between pins 1 and 4, with the automatic in PARK (or NEUTRAL). This sensor is the interlock that prevents the starter from running unless the transmission is in P or N. Must have continuity between 1 and 4 for starter to work. If continuity is there, reconnect the plug. If the harness does not look damaged, go buy a new starter relay, 'cause all that is left is wire and the relay socket.