Recently did a tune up plugs, wires, cap and rotor a few days after that I got CEL read the codes and misfire again, what could it be now?

Year of jeep? What plugs?

How many miles on the engine? Other things to consider:

1. Fuel injector. Swap the injector from the misfiring cylinder with another one and see if the misfire follows to that cylinder. You can also use a "noid light" to be sure that you are receiving a pulse from the computer to fire that injector.

2. Internal engine issue. Perform a compression test on all cylinders and compare misfiring cylinder compression to other cylinders

Its a 98 4.0 and the plugs I put in were the durlast I believe

Also misfiring on 1 and 2

I have a 2015 Cherokee Trailhawk. I am getting the P3301 error. Does anyone know what exactly causing this error?

You should try in the Trailhawk forum here:

https://www.cherokeeforum.com/f87/

Please make sure you post all of the codes and correctly. I'm assume you meant P0301 and not P3301.

Nope the code is NOT P0301. The code is P3301 manufacturer code. I have checked it multiple times to verify. So it is not a typo. I am trying to see if anyone else has received this code

Then you should try in the Trailhawk forum. XJ's (this current forum) doesn't list 3301 as a valid code.

Good luck.