The one you are currently using is the one I have in my Shaker 500 (Door mounted subs, Shaker 1000 also has trunk subs). How do you have it wired in? What head aftermarket head unit do you have? Do you have the Shaker 500 (door subs), or Shaker 1000 (door and trunk subs).
I have the Shaker 500, and installed this touch screen unit using that Metra kit you say you used and my subs work fine, better than with the factory headunit.
1966 Mustang Sprint 200--Wimbledon White
1998 Mustang V6 Coupe--Silver--RIP, Totalled by brother
2005 Mustang V6 Premium Coupe--Sonic Blue