I think its loose gears and has anyone tried no mufflers?

My question comes from my setup and whether or not it is worth to change. I currently have 4.10 gears in my '99 cobra and have no mufflers on the vehicle. This sounds amazing but I have to say that I believe I am loosing some torque . I also feel a small thump most of the time when I put the transmission into gear and when I let off the clutch. Now I have replaced the transmission about 5 months ago and am pretty sure it is not the U-joints so I believe the issue is with the rear end and something being loose but I don't know them that well.

Question one is if the rear end is loose would it be from the gears being worn so buying a new set of 4.10's would fix it? or would it be in the rear end and I have to rebuild it? How much should these costs installed/fixed?

Question two is by replacing the straight pipes with mufflers, say just 40 series Flowmasters, will I greatly feel an increase in torque? Has anyone else tried this setup, having no mufflers, and decided to go with mufflers?

sorry to ask again guys but just trying to get some good advice on whether I should replace the rear end or differential? or just rebuild it including new gears and other parts and how much?