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2012 Mk3 Focus S, 5SP, never tuned, 110k miles.

Relevant Mods:
K&N Drop-In
Optima Yellowtop (fairly new)
Mustang TB

Been an ongoing issue for a few months now, the start seems to have corresponded with the recall that was put out, and seems to have been made worse with the 2nd flash Ford did. I know one other individual having pretty much identical issues in their 2012 Mk3, which is bone stock, and I believe their symptoms began around the recall re-flash as well.

Symptoms are:

1. High Idle (1500rpm, on the nose): this happens more often than not, almost constantly. Occasionally it will idle correctly. There seems to be no rhyme nor reason. Hot day, cold day, nice day, cold motor, warm motor, full tank, empty tank, high altitude, low altitude... whenever the idle does eventually drop, it usually drops too far. Curiously, if I attempt to let the clutch out a bit while it's idling high, it drops very quickly and almost stalls, then rises back to 1500rpm. When it isn't acting up, I can get the car rolling without giving it any gas. When it is doing this, I can't. But if I get it rolling in 1st, the motor will wind back up to 1500rpm and I'll roll that way indefinately.

Sometimes revving the motor might get it to drop, but when it does it comes down very slowly, over the course of 5-6 seconds from 1500rpm to normal.

2. Rough idle/near stall: As mentioned above, this usually happens after it idles high for a random period of time. Motor will drop below 500 rpm, nearly stalling, before (I assume) the computer sees an issue and corrects momentarily, only to drop again. The idle "bounces" between nearly stalled and normal. Revving the motor seems to set it straight after a couple times, usually...

3. Another issue that has sprung up (after the vehicle was flashed the 2nd time) is ~60% of the time after I fill the tank, the motor will start and immediately stall. The motor can be cranked for 2-3 seconds and it'll fire back up, rev a few times, and all is normal. This happens irregardless of the fuel level before filling. Seems to be more common when I fill up with Chevron, but it just did it with with Arco gas for the 1st time.

My fuel level also appears to be incorrect, reading high over the whole tank. (Gauge reads a little over 1/4 tank, proceeds to take 10 gallons. Fuel gauge used to be accurate before flashing)

None of these issues throw any error codes. There was one occasion where it threw a code (forget which one, but it was related to high idle), but the light went out on it's own and after I cleared the code, it hasn't popped up again.

No noticable drop in performance, potential drop in mileage (hard to track when you can't trust your fuel gauge). I just fill up around 300 miles diven now.

Attempted fixes:

Cleaned air filter (k&n drop-in)
Cleaned MAF sensor (carefully, with special cleaner)
Replaced throttle body (upgraded to larger TB from Mustang, checked for air leaks and cracked hoses at this time)

No change in symptoms, for better or worse.

Spark plugs changed at 100k (~4k miles before all of this started) and noticed slightly smoother idle and better mileage for a while. Replaced with Motorcraft plugs.

It's probably obvious but I heavily suspect the new code Ford installed and perhaps how it's interacting with the anti-stall features. I'd just like feedback if anyone has similar issues, or has other ideas about what could be faulty and where to look next without just throwing money at the problem. Don't really have the money to pay for diagnosis/repair and would rather do it myself where I can. Any help would be appreciated.
 
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