HELP NEEDED - Ford operating systems?

[HulkdoutJK]

Hi all,
I am Erik, new to the forum and HP Tuners. I'm hoping to gain some knowledge on the use of HP tuners, along with light shed on the predicament I am in.

I bought a 2006 Mercury Grand Marquis LS 4.6L. I was informed by the second owner at purchase it will NOT pass inspection.
Exhaust was rotted so I replaced cat back, when I was building that exhaust I noticed they had gutted the CATs in the vehicle. The car also, has adjusted shift points and 3.73 final drive gears(axle).
I bought MPVIii, read my vehicles tune - installed credits. I was quickly able to identify the first owner had disabled the Catalyst and 02 monitoring systems. I re-enabled the corresponding systems installed a set of downstream 02 spacers; test drove for readiness codes. IT PASSES!!
Moving on - I work in a fleet management position and have access to FORD IDS at work so I decided to write to a factory PCM calibration to perform a comparison of what was actually adjusted in the vehicles current state of tune. HORRIBLE IDEA!

Since the update the Filename(as Ford calls it) or Operating system(per HP tuners) has changed. I went from FCFE6F6 to FCFE9F4, that being said I had to purchase licenses for the car because I lost the ability to write the PCM. This is where it went south.
It gets a bit confusing from here so I'll address the tunes as following:
HP tune(what I bought the car as)
Ford tune(what it factory flashed to using IDS)
Ford modified(me copying what the car was(HP tune) to the Ford tune/new operating system)

If I flash to the Modified Ford tune it no longer adjust the speedometer for the 3.73s gears - I tripled check to make sure I changed that parameter however while in editor and doing a comparison it still highlights green indicating there is difference between the two tunes but it is written correct as 3.73, which in term creating harsh drive ability concerns due to load calculation/ speed input error [I believe].

If I flash back to Ford tune and try updating my gear ratio using IDS it will not accept the gear ratio.

If I flash to the original HP tune the car goes back to how it was when I bought it, drives how it did speedometer is accurate. However, I now have a wrench light in my message center, NO P-code DTCs. I have a U1041 code Lighting Control Module - Vehicle speed signal missing or incorrect - FORDs pin point test informs you to disregard this code. lol
But all my readiness codes have finally passed today. I had to wait until we saw temps above 40F for EVAP to run its course.
Hopefully Tuesday ill obtain a fresh inspection sticker; then back to the drawing board to correct whatever the hell I got myself into here.

My next thought is to borrow a used PCM from wrecked police interceptor to write AS-Built data for my vehicle and see if my operating system/filename returns back to FCFE6F6.

I did read on the forum you can select operating systems to work off of, that seemed to only come up in GM talk.. But before I bore any of you any further with all the question and thoughts I have regarding this I'm staying optimistic that ill receive some good news and hopefully I made a correctable error.

Thank you to anyone who has read all this, I appreciate it!
Erik

[Thatwhite5.0]

It is possible you flashed a non compatible strategy. Post the tunes you have.

[HulkdoutJK]

It is possible you flashed a non compatible strategy. Post the tunes you have.

Potential TunerJoin Date

The tune was in the car to start with, all I changed was turning catalyst monitoring and o2 monitoring. That all switched over fine. Once I downloaded the PCM with OEM files with Ford's IDS scan tool, I began having issues. I know the operating systems changed numbers.
When you say post the tune, you want to look at the file I open in editor, correct?
If so I will load both of them when I get home today.
Thanks for the help!

[95Gturbo]

Are you just doing a write calibration or write entire? Write entire with the original tune should flash the OS back to what it was before. Write calibration doesnt change the OS, just the tune. Try a write entire with the original tune the car had in it.

[HulkdoutJK]

It is possible you flashed a non compatible strategy. Post the tunes you have.

The attached are the tunes I have.
1) what the car came with - I turned o2's back on.
2) what FORD IDS re-flashed the car to
3) my attempt to convert the Ford tune to what the car came with due to operating system differences.

Currently, i was able to load the tune the car came with back into the car even though its a different operating system, it wrote the tune and operates the car as when i bought it with the exception of a wrench light in my message display center. Today it DID pass inspection!

thanks

[HulkdoutJK]

Are you just doing a write calibration or write entire? Write entire with the original tune should flash the OS back to what it was before. Write calibration doesnt change the OS, just the tune. Try a write entire with the original tune the car had in it.

I am writing the entire tune, when in the write prompt screen I can only accept write entire tune. I think being the Ford Scanner changed my operating system it left a different signature in different module causing a wrench light on my dash message center even when i write the vehicle back to the original tune file.

[95Gturbo]

You should be able to check the OS of both files with in calibration details to see if it is different.