First thing to check is to be absolutely sure you do not have any leaks with your exhaust where unmetered air could get to the o2 sensors from outside. If exhaust is good and sealed/installed properly without leaks also verify the MSD intake manifold is properly "clamshelled" together. The manual has a specific pattern to tighten the bolts so it seals up without the gap that some are getting at the rear corner. ALSO, make sure you REMOVED the rubber insulation piece that was under the stock manifold when you installed the MSD. It causes the MSD to not seal properly on the head ports. Once all possible unmetered air leaks are ruled out proceed with below:
Are you histograming LTFT error vs MAF Hz? If so, do the below
Since car is already in MAF only mode, But you need to disable PE enrichment also. Change your PE throttle% to 100% across the board to keep it out of PE mode( DO NOT GO WOT!!! until you change it back to previous values!!) Do a log. Take car to an area with long straight to do the test. Stop car and start logging. In VCM scanner reset Long term fuel trims under Vehicle Controls and Special Functions button. Log car at idle for 2mins. Start to drive.. in 3rd gear or 4th(depending on how fast you are going at 4000rpm) do the following:
1) Slowly bring rpms up to 2000rpm rolling *light throttle* wait 5seconds then slowly increase to 2500rpm hold 5secs. repeat until you reach 4000rpm and hold for 5secs. accellerating slowly on each 500rpm jump.
2)Immediately slow down to 2000rpm again in the same gear... same log.. dont stop log and do the same 500rpm increments with a little more throttle this time than before.
3)Immediately slow down to 2000rpm again and in the same gear.. same log do the same 500rpm increments with more throttle this time but no more than 50% throttle.
After third test stop the log. You will use the histogram to view the AVERAGE error. Highlight the whole histogram values from left to right and copy to clipboard(MAF hz above 5000hz range should have zero for the values since you don't it that high part throttle)
Go into your tune under MAF Curve and highlight the whole table left to right then right click. In the dropdown box choose Paste Special and Multiply by %(Can do half% for smaller changes too). This should take the negative and positive error from the histogram and correct each cooresponding hz location on your curve accordingly up or down by percent error. Smooth any areas that may need it.
Save as a new file and load tune to the car. Go out and do the test again the same exact way. You want to continue to make adjustments until your LTFT error is +/- 5% or better.
Once you get your error to within +/- 5% and are happy with the adjustments *****
BE SURE TO CHANGE PE THROTTLE% BACK TO PREVIOUS VALUES!!!!!******
I also recommend NOT running MAF only mode. Change that back to MAF/VVE operation at some point also.
This is just to correct part throttle LTFT error. To correct maf transfer error for WOT you need to have a wideband o2 sensor and will histogram AFR commanded vs Wideband actual and make changes the same way you did with part throttle but to the WOT hz areas of the curve.
And just a note... JLT has been known in the Mustang world to SUCK at seaeling properly at the MAF sensor mounting point causing HUGE headaches for tuners. Make sure the sensor is properly mounted and sealing. Never was a fan of JLT on my Mustang. I used PMAS. On my C7 Grand Sport I have the Halltech CAI. If you are in a Camaro, the Rotofab dry filter CAI seems to have great results.
Probably long winded but bored in bed waiting for my sleep meds to kick in. If they had kicked in by now I would have typed something about Bob the 3 headed Goat telling me jokes.