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Just finished the "The Timing Job" on my 2004 F150 5.4 3v and I connected the battery to it. I put a multimeter on the battery and it read 12.6. No voltage drops anywhere. Checked some of the relays and fuses and they looked fine. Not sure where to go at this point.
When i try to crank it there is a click at the fuse box at the accessory delay relay(R02). i made a video to show it. The Crankshaft sensor is disconnected(for Priming purposes) and I switched other relays/fuses to verify that it wasn't a bad relay/fuse. I also checked to verify that the starter wasn't bad. Also the FPDM is new.
If your saying it will not crank, and was fine before you worked on it........ then I would RECHECK the battery connections.. Clean. make sure they are tight, and make sure you have a good GROUND......... after that, trace the positive cable from the battery to the firewall solenoid.. See if it has power at the input terminal.. When you turn the key, have someone measure the voltage on the output side of the terminal.. The small wire is from the key and should be hot and pull in the solenoid when you turn the key ......... and you do have the trans selector in PARK ? Try neutral and try wiggling it.. if you cant get 12 v to the small wire on the solenoid.
What does the battery volts do when trying to crank . It maybe collapsing ,since it has been sitting it may have given up . Try jump starting it or another battery . Failure to crank is usually not associated with a timing job .
Batteries only last 3 to 4 years on average ,its painful as a new high cca battery is not cheap . Lead acid batteries do not recover well from deep discharge .
If you have a no crank situation, I don't think it is security related, PATS disables the fuel injectors I believe. The click coming from the central junction box is most likely the starter relay. The starting system is pretty simple on these trucks.
Check Fuse F2.101 (labeled "Starter Solenoid" in the owners Manual) then Check for battery feed and control to the starter motor (the actual starter solenoid is built into the starter).
You can also try removing the starter relay from the junction box and verify it is getting control power from the ignition switch, but if it is clicking then it is.
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