I've gotten a few days to wrench on the TJ in the past weeks and have gotten several things knocked off the list. 

First up on the list was to replace the current Magnaflow 12866 with the newer and much larger 12276. I picked this muffler due to the center inlet and outlet and the case size being the largest I could reasonably fit in the space that I had. Check out the size difference in the 2 mufflers. If size is any indication of noise level, this should be a step in the right direction: 

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Before I could install the new muffler I wanted to delete the trailer hitch and rear stock rear bumper in favor of a low profile rear bumper with an integrated rear hitch. I looked at several units and ultimately decided on a Barnes 4wd bumper. After scuffing it with a red scotch brite pad, a few coats of self etching primer and gloss black paint later it was ready to install: 

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The bumper looked great but now the tail pipe and gas tank skid stuck out like a sore thumb. First to fix was the tail pipe. The muffler install went surprisingly smooth – the old muffler and intermediate pipe were removed, intermediate pipe was trimmed down and new muffler was installed in its place. I'll post a better picture when I can get the TJ up on a lift, but trust me when I say that everything fits snugly in place. Eventually I'd like to re-work the intermediate pipe to fit a little better but it'll do for now.  I wanted the tail pipe tucked up as high as I could possibly get it and after some creativity with the stock exhaust hangers, this was the result: 

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Bingo.

The exhaust hangers are temporarily permanent. The mount in front of the axle was clocked 90* to provide the lift that I needed. I'll drill and tap the second hole and this should work just fine.

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The rear mount is currently sitting like this: 

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The plan is to swing the factory frame side exhaust hanger forward, use the stock rubber isolator and attach it to a new hanger welded to the tailpipe. Speaking of tailpipe – I plan to either cut the current tip down or weld on a new tip that tucks up closer to the bumper. 

Next was to paint the gas tank skid. After a few minutes of prep with the Harbor Freight surface conditioning tool and a few coats of gloss black paint I had the back end of the TJ looking much much better. 

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 The next items on the list are to add another layer of insulation to the tub and get the A/C operational. I plan to do a detailed post on the A/C setup that I landed on. It's not terribly complicated, but did take a lot of research to finally land on a good solution that didn't cost a fortune.