Had ignition switch replaced and the key transponder won't crank the truck. Accessories works, starter doesn't. What can I do to bypass the ignition?

 

ignition switch isn't part of the PATS(passive anti-theft system) so wouldn't effect starting because of PATS, ignition switch is under the steering column.
Starter motor circuit also requires clutch pedal to be in all the way(clutch switch) or the automatic trans to be in Park or Neutral(NSS switch) for the starter to work.

Was the Key switch replaced?
This switch has a wire "ring" on it that reads a PATS key and sends that info to PATS module, if the "ring" was not connected or new key switch doesn't have the "ring" then you will need to hook it up or get a new key switch that has the wire "ring".

There is no way to bypass PATS easily or cheaply, that is the point of an anti-theft system.

 

If the new cylinder came with new keys (most likely) then the new keys have to be programmed in. Part of the design is that each key has a unique ID code that the computer reads at start up. The PCM can store 4 key codes at a time and if they don't match it kills the starter along with fuel pump/injectors on some models in case you decide to simply ground out the starter.

 

It is better to take a new cylinder to lock smith first and have it re-keyed to match original keys, so the doors, glove box, passenger air bag and starter all use the same key.
It is also cheaper than having the PATS module reprogrammed.

 

Screw PATS...

When I installed my new ignition cylinder I removed the PATS sensor ring, and placed the old ignition cylinder, key and all, inside the ring, taped it all up in a ball and shoved it down in the dash...

TADA no more PATS, and the cylinder can be replaced with one that the keys do not need any programming