Now I'm running the Shaker 500 w/ Z2 in my Mustang. I just bought some JL 12's and wanna run those along with the stock subs in the shaker 500. Is it possible like with running a Y splitter from the head unit? Or will this kill the sound quality?

yes you can run a y splitter. i did that on my friends stang with his d3. but you need to adjust the amp for the 12s in order to keep everything balanced. in the end it was better to just use the 12 in subs and not the 8s from the shaker system b/c you couldnt even hear them.