You can also try to recode the ecu with vcds for the manual trans.
If that doesnt work, I wouldnt hesitate to flash the other version on it, but the question for you is: do you know how to boot mode flash?
Check the both files with me7check and if things like bootrom version and file size are the same I would give it a shot.
Yeah I shouldve mentioned that I was unable to recode it with vcds. I do know how to boot mode flash but for some reason my pc wont detect it in boot mode on my bench nor will my laptop. Ill ground pin 24 for 5 seconds (I've tried up to 15 seconds) and when I go to read a file with galletto or connect in boot mode with nefmoto it wont detect, but it doesn't detect it normally through KWP2000 after grounding the pin either, so that tells me that it may be going into boot mode and just not detecting it. Thats why I asked the question of whether I can flash it just fine, cause if I brick it I wont be able to bootmode flash the stock file back onto it.