It is pretty easy although more involved than you might think just looking at it.
Since everything unscrews in the TJ (with one exception), the job requires very little permanent modification.
You'll have to remove and modify (or just replace ) the fan mount/grill in the caseroof as it will foul the motherboard after it's flipped.
The backplane panel is symetrical top/bottom and requires no modification but the channels that the tray panel slides in are different and do need changing.
The channel on the roof unscrews while the one on the subfloor is riveted and needs to be drilled to remove. * This riveted channel could be left in place- it's not needed for the swap. I removed mine because I had no intention of going back to stock...
These channels are not identical so you'll need to swap them- I found that the upper channel wasn't needed for stability, so I left it off.
The (formerly) top channel needs to go on the subfloor and will require spacing up to actually meet the motherboard tray (IIRC, about 3/16").
When you get the case, just remove the roof fan grill and flip the motherboard tray/backplane and you'll see what needs to be done.
Here's a small worklog from when I did this a year and a half ago.
Edit: A few tips about handling this case...
One sweet feature of the TJ is the fact that it's screwed together and that's going to make modifying it much simpler.
BUT...be very careful when undoing the rear struts that tie the open end of the main u-piece together.
That main section will want to spring open as soon as you loosen the strut screws, it's under a bit of tension as assembled.
Also, the sidepanel fit can be extremely finicky- I could barely slide mine off as it came out of the box.
Tweaking the screws on the rear struts can help alleviate this although I still consider it to be the biggest weakness of the case design.
Mine is a very early example and SS may have fixed this since, I don't know.
Also, be gentle with the screws that thread into the main chassis.
These are all blind threaded holes and the aluminum is fairly soft...you bugger them up and you're dead (or at least facing a PITA repair).



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