Here is the deal.I installed an Optima battery about a year ago..No problems. Later disconnect the battery to do some work. After hooking battery back up I started having idle problem .Soon I started hearing a knocking in the engine. Took it to ford dealer. They had the truck for 2 weeks ripping it down to replace cam, lifters, etc. When I got truck back, the noise was gone. But I still have rough idle and vibrations at 1100 and 1800 rpms.
I took back to dealer.

They checked everything from compression leaks to up date PCM.etc said truck engine is 100%.. I still have same problems.And prior to the work they did, I did not have the vibration problem. It may be a long shot, but after disconnecting battery you should go through a prosess of letting engine warm up operating temp, then run the A/C for at least 1 minute. Then drive 10 miles.
Could that be the problem? Is it that important?

 

By the way I cleaned throttle body and Mass air sensor..No change..It's really pissing me off!

 

Are these vibrations while the truck is sitting parked or are they while driving down the road? Is it throwing any codes? What engine? It takes the PCM a little while to retrain after the battery has been disconnected but not that long.