They diagnosed my CEL, and had my turbo replaced in 2 days.
Doesn't mean I was happy about the need to have it replaced, but it was done quiuckly and under warranty. There have been a number of turbo warranty denials by Ford, for people using aftermarket air intake systems.
Luckily for us, no one seems to manufacture one for the E-series. I would recommend that anyone running a non-stock filter swap it back to a stock filter though.
The variable vane turbos that Ford is using, haven't had the greatest rep. Once out of warranty, a number of people have gone with aftermarket turbos instead.
Good luck and keep us informed,