Alright first I want to start by saying even though this is my first post it is because for some reason my old account won't log in so I created a new one and thank you for all of your advice so far on previous post (on old account).
Also I have read SAMs noob guide
On to the problem/ problems?
Trouble first started when I was getting air leaking into the fuel system. I started by changing the fuel filter (it has the gen2 fuel filter head) and taking out the quick disconnect you can get to without dropping the tank. Didn't fix it so I went ahead and did a in tank lift pump with the IIRC airtech m7181e? Or whatever the one everyone on here recommends. I believe this fixed my air in fuel problem (it took a while to get all the air out of the system but has been air free the last 2 test drives) while I was doing stuff I noticed a antifreeze leak that looks like it is coming from my EGR cooler. Anyone had this problem before? That is item #1 that may or may not be related to what else I have going on.
Problem #2: It still has a stutter like it did with the air leak but it has a different sound to it. It seems like a missing cylinder to me so I was thinking maybe the air in the fuel system took out an injector. So I checked the return on each injector and they are all the same and don't seem out of spec on amount of return. (I didn't have a way of measuring 25ml a minute) but measured each one for 1 minute and they all seemed consistent to each other and about 25ml. So I'm kind of ruling out injectors unless anyone has anything else to check. The stutter is noisy and when in 4th or 5th gear at low rpms it shakes the vehicle.
Problem #3: this might be related to either 1 and/or 2 but it is putting out significantly more smoke then usual. It is black in color and does it under load not at idle. My jeep used to run very clean maybe a small puff when leaving from a stop. Now it looks like my old 7.3L ford used to... I was thinking maybe a boost hose (I haven't had a chance to pull them off and check for tears yet but they are OEM hoses and feel kind of soft just squeezing them). I thought this might relate to the stutter as well but not sure.
I believe that sums up the problems I'm having so now for some info on the jeep itself. It is a 2006 2.8L with about 118,XXX miles. Had the timing belt and water pump done at 110,000 (I know a little late). I do oil changes regularly with rotella T6 5w40. I drive a lot of highway and I am very easy on the throttle. I just did the EHM when I did the lift pump so it probably doesn't count. I don't have a GDE tune yet, I was literally going to order one the night it started acting up
I think that pretty much sums everything up anything I left out let me know. Thank you for any advice.