It sounds like you have problems that can only be corrected by some slightly drastic steps. The first I would try is to on into the Clockwork thread that has already been linked in this thread. In that thread is a link to the new full Clockwork backup. You can use that to do a nandroid restore and I think that will help your phone dramatically. There is something wrong with your phone and or the root.
If the above doesn't solve your issues, then there are zips now to return your phone to bone stock. If it is still slow as a stock device, you need to return it. But I really think one of these flashes is going to solve your problems.