m6 swap programming & JET SCU ?'s

Iam getting ready to swap out my auto for a six speed, now i know the pcm will need re-programmed but theres a few complications.
First when i got the car it had 3:42gears and the speedo was roughly 20mph fast but it shifted fine. Then a local garage put a JET SCU2000(link) (http://www.truckaddons.com/Catalog/subpages/JetSCU02.htm) on it to make the speedo read correctly. Well when they did that it made it so the tranny wouldnt upshift under full or even half throttle. After i put the 4:10s in it the garage used the JET SCU to get the speedo to where it was 'only' 25mph fast and it still shifted like crap. Said thats the best they could do.
I played with the 4 settings on there and wrote down the settings to make it upshift right, only problem is when its set like that the speedo is about 50mph fast.
Now the reason i wrote all of this out, after i have the six speed in, what do i do with this JET SCU thing? If i have the PCM re-programmed will this thing still make the speedo read wrong? Would putting all of the settings on ''0'' perhaps put it back to whatever stock would be and let the reprogramed PCM do the job?
Also can madz28 tune for the m6 swap, gutted air pump and removed emissions stuff?
Sorry for the long post, i just want to make everything as clear as possible.

Thanks for any/all replies!! :bow: :bow:

When you get your pcm programed for the 6 speed have it programed for whatever your rear end ratio is and you won't need the Jet SCU. I'm sure any of the programers can do it. When I converted mine I used Tunercat and did it myself. You just need to put in a 6 speed program.

So do i just un-plug and get rid of the JET SCU thing after its re-programmed?
I dont have tunercat or lt1edit so iam gonna have madz28.com do it and also set it for headers and emissions delete and stuff like that.

Thanks! :bow: