fingertapper,
Its hard to diagnose your problem. It could be the guitar, or the pedals, or the pickups or the strings, etc. But dont forget the amp which you dont have.
Try out all the suggestions on this thread but I dont think one factor will solve your problem. Before I tried a stock MT2, I had no problems with it even on low settings because I already had the right guitar and amp. In short, baka ok lang current set up mo pero you dont have the right amp. Before you try out any mods wherein you are required to spend, make sure may test unit you can match with your gear. Once modded ang MT2 mo at hindi mo magustuhan at pumanget and tunog, wala na iyun. Ang hirap na ibenta and you have nobody to blaim but yourself.
Mahirap kasi mga one size fits all solution lalo na kung hindi pa nakita ang buong set up mo.