'01 F250 2v 5.4L vin L 2wd with 4.10 axle

You guys have seen my post about the negative fuel trims, tho it turns out that this issue has actually improved the operation of the truck. I am still having high negative long term fuel trims but the trucks acceleration has improved quite a bit and the transmission is shifting much much smoother, often shifting without me noticing. According to my new bafx scanner paired with torque pro shows that my fuel economy is up, by about 30 miles per tank which I will verify with next fill up.

Only thing I'm still having an issue with is a slight miss at idle, which is not showing up as a misfire according to torque pro - I am open to suggestions to a better app, my innova 3160g shows info on misfire for each cylinder and torque pro or my bafx dongle is not reading individual cylinders, it's only showing total misfires at 0.

My intake air temp is reading roughly 25°f warmer than outside temp,
coolant temp 186°f,
CHT 218°f,
manifold vacuum at idle 24.1 in/Hg,
LTFT at idle -10.9 both banks which is an improvement from -25 (possibly dirty MAF? Or PCM catching up to new intake manifold? Outside temp was around 67°f at time of reading).

Here is a screenshot of the last reading before shutting off truck

 

I worked on a friend's 5.4 and he had a slight miss at idle also, I purchased a COP tester and made figuring out which COP/spark plug was the culprit. I ended up buying an excursion with the 6.8 V10 in it and ended up using lessons learned to fix the same issue on it. Might want to give it a try, thay can be had for around $35 on ebay.

 

Out of all the COP problems I have had I have never had one throw an engine code. A COP tester would definitely make the job easier, but you can also pull one coil at a time and whichever one does not change your idle is the bad one