The plugs are not likely to make enough of a difference to make the car run like crap, although you do want the best plugs for your app, once you get it sorted out. I agree w/Rod-when you run into a problem like this go back a step and try to remove as many variables as possible before proceeding to the next step. My experience w/JRSC ovr 2 1/2 years is good-it has to be something you did or did not do properly. The only problem I have had w/the JRSC is with the t-taps used on the MAFS-they didn't make good contact. Check continuity from the MAFS harness to the output from the t-tap. Check the fuel pressure regulator hookup also-did you hook those up correctly? Double, and triple, check your install per the JR instructions. Things to look for-unmetered air from a vacuum leak somewhere (back of the JR manifold, one or more of the vac hoses on the top of the blower, vac leak at or around the TB. You will need longer screws (1.25"-I got mine at Lowes) to properly secure thew 65mm TB to the JR blower flange. Don't use any type of gasket sealant there-you do not need it if you install the TB correctly. Small vac leaks will wash out at cruise or WOT settings, so your problem may be more than a small vac leak. Is the EGR vac hose hooked up right? how about the other small diameter vac hoses that hook up to the top of the blower? What about the large diameter air intake hose from the MAFS to the TB? is it tight? what type of air filter are you using? There is a history of problems w/MAFS funky from too much air at the wrong time/place.
When you get it sorted out, and you will, put that 65mm TB on. It really wakes up the JRSC!
Good luck-keep us posted.