I think you need to slow down a bit with the diagnosis before jumping to a compression test. I think you jumped the gun with replacing the O2 sensors and possibly the y-pipe/cats.
You need to start by diagnosing the misfire first, I am willing to bet if you fix the cause of the misfire, your other symptoms will go away. Like was mentioned earlier, hot cats are either caused by being plugged or by raw fuel burning in the cat itself. Since the cats are new, its probably safe to say they're not clogged. So now that we've ruled out a clogged cat, we know the other cause of a glowing cat is raw fuel, we also have a misfire code as well. Misfires are either caused by a fuel issue (leaky or non-functioning injector), a spark issue (bad coil or plug) or a mechanical problem (bent valve, dropped seat etc.).
What cylinders are getting the misfire codes? Start by checking plugs in those cylinders. If the plugs are wet and smell like fuel, ensure the coil packs are working. If you're getting spark, test for leaky injectors by pulling the rail and turning the ignition to 'On'. This will pressurize the fuel rail, watch for any injectors that are stuck open or dripping. This can take awhile, so you'll want to watch them for at least 20-30 minutes while the pressure bleeds off the fuel rail.
If the ignition and fuel systems are working properly, then go ahead and do a compression test. If you have a scope/camera you can look inside the affected cylinders for piston or valve damage as well.
'00 WJ 4.7 Limited- Some stuff
'03 WJ 4.7 Laredo- Some more stuff
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It is what Jeeples has *PARTIALLY* stated.