2011 2 door, manual transmission

So, my engine light went on this morning and then went off. I checked for the code and there was no code...just did the -------- and then said -done-. Went about my business and then the CEL went on again at the end of the day when I was almost home and started flashing non-stop. The Jeep began shaking violently and I thought it was going to stall, but it didn't and continued to shake the whole Jeep. I stopped, turned it off, let sit for 10 mins then turned back on and still the same trouble when I got to 2000 RPMs. Below that, the light would stop flashing but would remain on with the Jeep running really rough. I drove it home, which was right around the corner and parked it...the whole time with the CEL on or flashing, based on how high or low the RPMs were, and running roughly. Having it towed to the shop in the morning.

Edit: after I posted this my neighbor let me use his code reader. Here are the results:
Stored codes:
P0325 Knock Sensor 1 Circuit
P0420 Catalys System Efficiency Below Threshold
P0305 Cylinder 5 Misfire Detected

Pending codes:
P0420 Catalys System Efficiency Below Threshold
P0305 Cylinder 5 Misfire Detected


Backstory: Just replaced this engine 4,300 miles ago with a remanufactured engine. At 975 miles I started having the CEL come on intermittently and I got the code for "knock sensor". Took it back to the shop and they stated that a spark plug wire had been pinched in the install and they replaced it. The problem went away for about another 300 miles and then the CEL has come on twice since (in about 3000 miles) with the same code of "knock sensor" each time, but went away at the next restart. Haven't had the CEL come on now in at least 1500 miles since.

Fast forward to today and I'm curious if these two are related. Never had the poor performance and the light never continuously flashed either until today.

SO, I've done some reading...sounds like a misfire. I called my shop and the mechanic stated that in his experience with this flashing CEL on GMs (said he has never seen it on Jeep/Chrysler) that it means that the engine is misfiring and that fuel is dumping in to the Cat. WTH??? I have a 2 year warranty on parts and labor on this remanufactured engine. Would it cover something like this typically, and if it's my cat would it cover the damage done to it due to the gas dumping from the engine due to the misfire?

Any feedback or contrary opinions? I honestly don't know much about engines other than what I learn after I have problems. And now I'm totally freaking out because I'm told this could be "major engine malfunction".

Feedback/opinions are appreciated on ideas of what this may be and other opinions related.

Additional issue below:

I'm also getting some clutch chatter going in to 1st and in Reverse, but ONLY after the engine is nice and warmed up, and usually after driving for about 25 minutes. I tend to have to get on the accelerator a bit more to get through the chatter going in to first and the whole Jeep shimmies until I'm completely rolling and through the first part of 1st. Cold out of the garage it doesn't happen for a while. I had a new clutch put in when the engine was replaced. Flywheel was machined, clutch kit for the rest. I'm stumped at the fact that the clutch chatter isn't there all of the time. This has been happening since I had the clutch installed. I thought it was just from not being used to the new clutch, but it has been persistent. Any ideas? This can't possibly be related to the above, can it?

 

I am surprised there are no responses to your post. What was the resolution to your problem? Hoping to find a solution that I can fix myself.