Most of the issues with the coil packs were resolved by the time the gli with the 1.8T came out as the "new" parts everyone was getting replaced were stock equipment by then. I also don't know how you expect your warranty to be covered when you modify your car from original spec and something breaks. I agree the two things may not be related, but what would you do if the situation was reversed and you had someone show up for warranty service because their car was broken and they had a bunch of modifications? First blame for all the issues will go to the modifications, based on the "whats changed that could cause these problems?" troubleshooting methodology.
Now on to my suggestion, if you're looking for something to modify and be "fast" in you might as well pick a new car unless you're ready to spend some serious money and still only be sorta quick. If you're still stuck on the vw get the vr6, you will be a lot more happy in the long run and imho more reliable although it won't look as slick as the gli.