Initially with my 511iR I had an issue with the TPS (Throttle Position Sensor) going out of calibration and giving an idle that was inconsistent and high. The TPS was recalibrated by computer and worked fine for awhile then went out of calibration again. I was ready to take the car back to the shop to have the TPS perhaps replaced when for no apparent reason the idle has been spot-on and consistent for the last week or so. A breaking in problem? Dunno, but it's coming off RPM and going into a nice stable idle just fine now. We'll see...
Also have an issue with an occassional misfire when punching the throttle after the engine has been at a steady modest RPM for a couple of minutes. I don't know if this is a problem of the engine getting loaded up or what but this too seems to be getting better and less frequent. This needs to go completely away though because sometimes (rarely now) the misfire is more dramatic and startles me when it happens -- not to mention it must be hard on the engine. So long as it's getting better at a consistent rate I'll hold off on having the curves tweaked to see if this too may be a break-in issue that goes away.
The rear main seal leak issue with the Roush FE's so far has not been a problem for me but is an issue Roush is working on and I wouldn't be surprised if that issue rears its ugly head to me too -- again, we'll see. I do think I have a small
oil leak in the transmission where the speedometer cable attaches and will have them look at that at the shop, but that's not engine related.
I'm at about 375 miles total and these are the issues I've had so far. As this engine is breaking in I'm liking it more and more and the pull is great. Dyno'd at 607/595.