Please Help: Power loss/jerking issues!

Okay so hears the deal:
2005 Mustang GT, manual, only 54k miles on it

Things to consider: Just replaced my stock mufflers with flowmaster mufflers

So, when I shift into and out of 2nd gear and occasionally 3rd you can hear what sounds like grinding... but I cant really tell if it is grinding.

Also, when I am in about 1500-3000 RPMs, my mustang tends to jerk and loose a lot of power, almost as if it doesn't want to inject fuel. Feels like a giant or something is pushing back on my car, not allowing it to accelerate.

I used a Mac Code reader to see if it was an oxygen sensor or anything of the nature but no codes were thrown on reader.

Things I have done to try and help the problem:
Replaced Air Filter
Added Sea Foam to fuel
Checked Diagnostics
Felt Clutch, felt tension at about an inch to an inch and a half

Please help me out if you have had this problem or something like it, or if you know what might help fix my mustang.

Really appreciate any help I get. Thanks guys.