PCM replacement with headers and smog delete
 

94 F350 460. I am going to replace the PCM. I have headers with no cat and all the smog components have been removed. Can I replace the PCM with factory programming? Will having headers and no emissions stuff cause issues with the new PCM?

You will have a check engine light on and a number of codes for the EGR unless you can source a Twisted Smog EGR harness from a garage sale. Ebay won't even allow them to be listed anymore.

I have the egr hooked up. The set of Headman headers I’m running have the egr hookup.

I thought no smog components meant none at all. If that's the case you may still have a CEL for the thermactor. It won't drive any different just might smell a little rich on startup.

Why? is it having issues?

No, the air injection system has no effect on EFI operation and a free flowing exhaust isn't enough of a change to cause issues for the factory "tune", but you must install an O2 sensor in the passenger side collector and there has to be some kind of exhaust behind the headers.
There will be codes set for the missing smog components but none of them besides EGR are significant enough to set the check engine light. If you block off the EGR.. sandwich a piece of metal between the valve and intake, but otherwise leave it functional with the position sensor and vacuum line connected and the EVR solenoid in place and connected, you won't have any codes set. This version of EGR doesn't measure gas flow through the tube so it won't matter that there is no tube connecting to the exhaust, the computer just looks for valve movement when commands are sent to the EVR to apply vacuum to the valve. That is why these components must remain and why EGR eliminators don't prevent a check engine light.

Only issues is a very dim battery light and 1500-1800 rpm slight studder that cleans out immediately when you get in the gas. We have done every check and test on the battery light. All grounds, wiring and voltage test good. Fuel pressure is correct.
The reason I think its PCM related is because we pulled it last week to inspect. I cleaned all the connectors and pins. Opened it up and cleaned all the dust out.
After putting it back in the 1500-1800 stutter was less noticeable and the Battery light was very dim. Now the ABS light is on after cleaning.
Truck sat for 5years in the Vegas desert with the motor out, so not sure if that could have an effect on the PCM.
We do have the O2 sensor hooked up and no CEL light on after correcting the vacuum line routing on EGR. Thanks for the reply!

The ECU/computer has nothing to do with the battery light or ABS operation. The ABS has its' own standalone module.

The electrical charging system has no reporting to the ECU.

The thing to look for on the computer board is corrosion under & down the legs of the blue can style capacitors.

Looks/acts just like leaking dead batteries left in a flashlight or other device.