My truck is throwing code 41 (Generator field not switching properly)
and 12 (Battery connection disturbed within the last 50 starts) from the CEL, would you say that it's the alternator going bad?

 

I'd swap the ASD relay for the A/C relay first.

 

What you mean?

 

There are three relays mounted on the inside of the left fender. Swap the relay closest to the battery with the one closest to the hood hinge.

If you problem goes away. Replace the bad relay. If the problem doesn't go away let us know.

 

So, i switched the relays around and then went junk yard hopping today and the light still came on, but on my way back from Lebanon county my radio kept turning off and on, and then I noticed that my voltmeter was low on the dash. So I drove with no radio. When I got home I took a voltmeter to the battery and it was putting out 9.75 volts and then I tested the alternator and I didn't even get a reading. So yeah

 

GOT IT! One of the therminals on the back of the alternator had broke so I disconnected that part of the wire harness and resoidered it, check engine went right away!