Oh where to start...

I first starting having issues with some of the electronics...turns out my battery was nearly dead. Replaced that and it fixed a few of the issues/codes.
Issues that are still lingering
-Severe vehicle shuddering at idle and low rpm accelerations. Bad enough where I don't want to drive on the interstate.
-Check Engine light is on. Reading a misfire on cylinder 1. I had recently replaced all spark plugs and coils since I was having similar issues not too long ago. (the spark plugs were nearly black!) The truck ran great after the plug/coil swap.
-Weird whistling sound after i let off the gas. It isn't the normal turbo sound (not like you can hear that much anyway)
Any ideas? I'm on the hunt for a good Ford mechanic in my area since all of the dealerships are garbage.

 

Drill weep hole in intercooler, check your plugs again, you may have a hairline fracture in #1 plug even though new.