Could be a mount left loose, but also check to see if the headers or exhaust is making contact with anything (frame/body/steering shaft) I've seen it before, where headers have been installed, one of the headers was making contact with something causing a "vibration". Had that problem with one of my trucks before, the drivers side header (long tube) was about 1/16 to 1/8in to far over (due to the primaries not being bent enough) which made it hit the frame and give me a vibration. This may not be your case, but its worth a look.

 

08SC's opinion makes sense to me as well. If you had no problems until they messed with your exhaust, then your exhaust should be the problem. Crawl under and check for clearance issues. The new headers may look great at the engine, but could have thrown something down the line out of tolerance. The header bolt re-torque should not really be an issue just yet.

 

Also, if you see nothing that is making contact, it could be that the exhaust is bound up. In that case, you'd need to neutralize the exhaust system, loosen all clamps and flange nuts/bolts, let the exhaust hang free then re-tighten, or start it up and see if it vibrates before you tighten. I've had this happen on some Fords before, not after a header installation, but it could still very well apply here. If all else fails, it may just be how the truck runs with the new headers, unless it's a bad vibration, it shouldn't hurt anything, and if it just gets on your nerves, put a damper right after the header if you've got room, that may absorb the vibration.

 

Thanks for the advice, this seems to be a very plossible reason for the vibration, I'm going to have them go through the whole system today and see what the F#*k.