Thud from the cargo area.
 

I have a 2016 Jeep Wrangler Unlimited, 4" lift 35" tires, also installed a Rugged Ridge Spartacus HD tire carrier kit for the added weight. When I added the tie carrier it removed the rattle from tailgate. Also removed the jack and tire iron (cant use it anyways) thinking that was the thud sound I heard. I don't hear the thud all the time, just over some bumps, not all. I also removed the trey under the cargo mat

Any ideas of what next?

If it is just over bumps I would have a look underneath and check out your suspension and make sure nothing is binding or contacting other components.

You may want to look at the clearance between the track bar and rear spring. Welcome to the forum.

I had a few rear end thuds from late night part installs. Check all torque on anything that moves back there. My issue turned out to be that forgot to tighten up the end link and lower shock bolt on passenger side and once I torqued down all was well again

I had a clunking noise in the back of mine that took almost a month to find. It sounded like the jack was loose too. After checking every part I thought it could possibly be several times I accidentally noticed a few chips in the paint on my rear bumper. Turns out at body flexed on its mounts it was hitting my barricade bumper. If you have an aftermarket bumper it's another thing you can check. Mine had a little clearance at the pinch seam but was hitting the body right above it.

It's relative
 

I'm not familiar with the design of your bumper but my previous generation Rugged Ridge rear bumper/tire carrier was hitting the right side of my frame over bumps. I loosened the bolts, had the sister in law (who weighs maybe a buck and a quarter) stand on the right end of the bumper and retightened. Problem solved.