Having issues with a 2009 manual 6.7 please advise....

Hey guys,
I've got a 2009 Cummins I'm working on tuning for a remote customer. It is a manual trans truck, and it was very difficult to obtain a stock manual trans file for this truck but I finally got my hands on some....

We couldn't upload the stock tune from the truck, it apparently had another tuner on it. The owner was unaware as was I until we tried to read it.... we also know this because even though the DPF was in place all sensors were unplugged.

Of the two stock tune files I was able to obtain, both say "Tune file analysis, incomplete do not flash" in V7.5, however in V8 they report "OK to flash" I have attempted using both of these files to overwrite the ECM and have experienced intermittent issues.... not certain that they are caused by the above mentioned concerns or not.

The truck will sometime rev up and hang RPM's between shifts when clutched, and then sometimes it doesn't. One time we'll flash a tune in, it'll run okay, next flash it's back to revving up.

It also sometimes throws a P0601 and the dreaded red lightning bolt is on after the most recent flash attempt, truck still runs and drives... but I understand this could be the "end of life" code for an ECM, but then some people say they can clear it or flash in an update and make it go away?!

So my question is mainly this.... do I go with the V7.5 file analysis or the V8 analysis? I do have a 2009 stock file that is 100% un-corrupt and says "analysis ok to flash" in V7.5 and it was used to tune the truck with which it was read from... BUT it's an auto trans file, will it work on the manual trans truck? I tried once with an 08 to flash an auto trans tune into a manual truck and the alarm went off as soon as it started up... may have been another issue but I'm gun shy now....

Any advice would be much appreciated, we are currently considering the possibility of having the dealer perform a "master reset" flash to return the truck to true stock, but I fear the unknown; will it be returned to stock with an "anti-tuning" bootblock? No way to know beforehand I suppose?

Thanks for any advice and information on this topic.

Flash in a 2008 Man Trans file.

I've had 0 issues with older files.

Had this same issues myself last night. had a clean 09' file and it wouldn't flash in, diasabled the checksum and got the p0601, flashed in an 08 clean file and no issue after that. no you can't flash an Auto tune into a manual lol aske me how i know. I accidenmtly selected an auto tune and flashed it in a manual once and when i started it the gear select display showed up in the speedo, and warning lights and dinger was going nuts. flashed the right tune back in and all was good.