OOOOHHHH Boy ,I have been in you shoes. Rattle, Rattle, Rattle.
It is a FREAKIN pain bro..I know.
I have this system on my car now and love the sound and performance. Today it set a few alarms off in a parking garage as I was driving through

.
Here is what I done w/ mine, ran the system for a while to let it settle out.
If it was like mine it is only tapping/rubbing in 1 small area and it does not need much.
Get back under the car and loosen the clamp on the connection between the cat and muffler. Leave the over the axle pipe to muff clamp on the muffler tight and only manipulate the one by the trans tunnel.
Try push/pulling and twisting the pipe connection I spoke of to get a little room. If you get room by manipulation then keep it held,twisted, etc in that spot an lock that clamp back down this may require another person to hold pressure/whatever while u tighten the clamp back.
Also, look at the exh hanger coming off the trans mount over to the cat and see if the rubber is pulled tight keeping the pipe up.
If so get a prybar and bend it down a little(don't get crazy) just some and see.
Another place is where the muffler mounts too the body.
U can put some sort of spacer between it and the body to give you a little room.
It takes time but just fiddle around with the above mention things and you will get it.
Did your pass side pipe coming out the muffler reach the hole in the frame?
Mine was short a few inches short, so I used one of the rubber hanger pieces that came with the system drilled 2 holes in the rubber strip and used that to bridge the gap from the hole to the pipe. And you can not even tell at all.
The pipe hitting the floorpan and that pass pipe being to short for the hanger was my only real problems.
The Pipe tips polish up nice with some effort and really gleam.
Good luck, let me know if it works.