A couple weeks ago the g/f and I took a vacation to Mexico. For the first time since the Cougar's resurrection, the car sat for two weeks. I've been driving it nearly every day, and never a check engine light in almost 25,000 miles. My g/f drove the Cougar to work, and guess what. CEL comes on.
I check the codes, one for IMRC stuck open, another for failing DPFE (P0401). The code for the stuck IMRC happened a few times immediately after the engine swap. It turned out the IMRC cable bracket was slightly bent. A little "encouragement" and no problems since. I have no idea why the code appeared now 2 years later... but after clearing it, it hasn't come back.
I thought maybe these hiccups were just from sitting, and my g/f's inability to drive the car as it's meant to be driven (like it's stolen!!!). She's also used to driving our 2012 Jetta TDI 6 speed, which is very different. I cleared the codes which remained gone for a few days.... then P0401 came back. The DPFE is an original part, with 99,xxx miles on it now. I'm guessing it just needs a new sensor.
This 3L hybrid (which I built from leftover junk parts) and rod shift Quaife (built by TH) drivetrain have nearly 30,000 miles now. Less than 5,000 in the '97 Contour, and now 25,000 in the '02 Cougar. And this is the first real issue. I'm quite pleased :)