Offshoreonly.com - Ignition and program upgrade

I have been down this road.... the MSD will not give you any more HP or MPH that you will notice. It will give you better idle and maybe clean up the black transom soot.
The ECM is already factory programed to optimize the stock engine. There really isn't a whole lot to gain by reprogramming the ecm without doing any other changes. The first round modifications for this engine should be better aftermarket exhaust, add an adjustable fuel pressure regulator so you can up the fuel pressure a little and add a good K&N flame arrestor....and then reprogram the ecm to take advantage of these changes. This combination will give you a little more power...but I think that 50hp is too optimistic...and in my opinion 3mph is also not realistic with just these changes.
Keep in mind that there are only 3 or 4 companies in the whole country that can remapp a mercruiser ecm and it costs about $350. I don't know who your local shop is but more than likely they would have to send it out to one of these companies to be remapped. Jim at Arizona speed and marine and Mark at Precision are 2 of them. Tyler Crockett is also very familiar with modifying these engines but I'm not sure if he actually remapps the emc's himself ?? The MSD box and harness are about $300. Sounds like your local marine shop is charging too much and throwing out unrealistic performance #'s. I would be VERY LEARY about letting any local shop touch my ECM's. One slight screw up and your engine is toast! Hope that helps.