Rough Idle Please help ghost issue

OK, I will begin with "Some of you might think I am Crazy" But here goes!
I bought this 2003 GC 4.0L dirt cheap because it needed an engine so I put a re-maned Engine in it. I know its alot to read but if anyone has had same symptoms or info on this matter please share!

Issues
1) It has a rough/choppy idle, not as bad as a misfire but its definitely noticeable. It is not high or low (sits about 500-600 when warm), just rough!
2) If its idling in park/neutral and I tap on the gas pedal real quick it dips before coming up like its going to stall but never actually stalls.
3) Really bad Gas Mileage (7mpg around town, 16mpg highway... should be 17/24) also the overhead info center that tells me the average mpg is way off (too high). and Fuel trims (short/long) are about +5/-12.5% at idle and 0/-7% driving.
4) Although the idle is at good rpm it is very strong. It takes a lot of pressure on brakes to keep from moving. it can climb up hill with a loaded trailer behind it with my foot completely off the gas!
5) VERY rarely I get almost misfire feeling when I'm driving on the highway only happens for a split second. maybe once every hour of driving with cruise control on, not too worried about it.
I THINK ALL THESE ISSUES ARE RELATED SOME HOW!

New Parts and other things I've done or related Information
1) Engine
2) Plugs (and Swapped coil pack with different one, no change)
3) Set of NEW BOSCH 12 port injectors (instead of stock 1 port) because they are said to improve smoother idle, throttle response, power and in some cases improve fuel economy. (no change to rough idle, in fact i think mpg got worse)
4) Throttle Pos Sensor (swapped Idle air control motor with new one too, no change, sent it back) Cleaned Throttle body and intake was scrubbed when engine was out.
5) Fuel Pump and filter/regulator
6) Smoke tested for vacuum leaks, only thing i find is the throttle body leaks a bit but I'm told its normal
6) i turned the camshaft pos sensor while looking at my scope to determine it is within 2 degrees +/- of perfectly 0 so ignition timing should be timed perfect.
2) my fuel pressure is 51psi key on 55-57psi running
3) no codes to go off besides (P0445 "large evap leak" which is a ghost too cause i cant find it even with smoke test and it comes back at random various times example. over night/ 1 week/ 3 months/ 1700 mile trip)

Now here is where ya'll gonna think I am crazy but hopefully not! I am a mechanic and i do know ghost stories exist even if I "Cannot duplicate customer complaint" as the dealerships like to say.

I live in South Florida. Sea level / 70-100 deg F / 80-100% humidity year round.
I just took a trip to Cherokee North Caroline up in the mountains, elevation 2k ft and it was roughly 30-50 deg F the whole time I was there and...
THE ROUGH IDLE AND "STRONG" IDLE WAS COMPLETELY GONE!!! For my entire stay!
I pulled into the campgrounds and the idle was so smooth I couldn't even tell the engine was running! The idle's strength felt like any other car I've driven, had to give it gas to move! One thing strange i did notice up there though was that the EVAP purge vale was running at idle which i do not believe should happen at idle, It was audible even in the driver's seat with window/door/hood closed. clicking away.

My VERY first stop for gas/snacks in Florida... the issue was present again! This leads me to believe that there is an issue with the MAP sensor reading the wrong barometric pressure. My dad (mechanic shop owner) says that some cars that have sensitive MAP sensors that live in the mountains can be running fine until they climb into a lower barometric pressure and run like crap until they are shut off and restarted so the MAP sensor and redetermine the pressure. BUT with my scope i can see that the sensor is reading 766.66mmHg which is about 14.82psi which sounds correct for my location? Should I replace it and see what happens?

I have been battling this issue for months now but on a separate note, Just this past week i have been having intermittent communication errors. when it happens it causes the dash to freak out, electronics such as AC blower and headlights not to work (still starts, runs and drives fine most of the time, sometimes stalls). all codes and symptoms point to a bad PCM so I might have to get that swapped or fixed soon if it keeps happening. Could the PCM be causing my idle issues as well?? battery (which i have not done)? alternator??

Please let me know anything you know on the matter! and i will answer back to questions asked and post the solution if i figure it out! thank you!

 

you have a SCANNER great!
FYI it is recommended you use oem/jeep for sensors if any.
What plugs are there?
I always like to look at ECT, MAP, TPS, o2 sensor B1S1 voltages and Fuel trims;
Your fuel trims are HI with the correction over 10, a place to start...

Is there a fuel schraider valve on fuel rail?



My dad (mechanic shop owner) says that some cars that have sensitive MAP sensors - common pooor tolerances and reason to recommend OEM, yeah the cost a little more....

P0455 - the valve running is located underhood left front fender. Do you have bidirectional control with scanner - so many preconditions to runn a EVAP check....
>>>> a thought You do NOT overfill the tank after pump kicks off? Gas gauge is OK?

Your new dash lighting issue any new codes "U" ?

 

>> I'm not sure what brand the plugs are but like i said they are brand new (bout 5k miles just like the engine). But i was thinking about changing them anyway. My dad says the brand "Champion" is kinda crappy for most cars but they are OEM brand for alot of JEEP/Chrystler for those years so i was thinking about trying Champion since i can get them cheap through the shop and put them in myself. Thoughts on Champion?
>> Yes there is a schraider on the rail which is how i found that i had 55-58psi.
>> I have not looked at the O2 sensors yet, im not very good at reading them to tell if they are bad but i should definitely look at them soon (its my wife's daily driver so i don't have it at the shop every day)
>> I'm not sure what you mean about bidirectional control but the scanner i have does have a command to test the evap leak (run the pump) no matter what the running/driving conditions, and im pretty sure i can hear the pump running, it even makes a beeping noise until its done. My father and the manager here said they chased one down a while back with the same code but it turned out there was no leak but the PUMP was bad?? and no i do not over fill the tank, but every other time i fill the tank, at first start up it starts hard (long crank time, and VERY rough idle for about 5-10 seconds) then is fine after.
>> As far as my new issue with the controls/dash, There were TONS of communication/"can bus" codes in almost every module in the car. I cleared them ALL but 1 would not go away. it is in the ABS module and the code is (you guessed it) U3FFF05

 

by the way, thank you for taking interest in my very long winded topic!

also, since i cleared the codes for communications (maybe 3 days ago) it has not happened again where as before it would happen 1-2 times per day!

 

yes champion plugs are suggested for the 4.0L, and yes I also do not rate them as high quality- but try to go with Champion they work here. Remove and read them wet, dry, black, tan ?


"I'm not sure what you mean about bidirectional control but the scanner i have does have a command to test the evap leak (run the pump)" this is exactly where I was going EVAP test run infrequently - many preconditions SO a scanner helps.

I asked about the schraider valve to test fuel pressure AND turn key to run, observe pressure rise then leaving KOEO observe pressure drop... drops Xpsi in 5min....post. Pump only runs @ 2seconds eng off.

Get a scanner on and look at ECT, Fuel trims long and short, B1S1 o2 sensor voltages, MAP, and TPS.

Any issue with cruise control is SRS light on?

Now that U3FFF05 - that code does NOT appear in my search engine AND jeep OEM manuals also searched
Suggest you give me the description the scanner attaches to it.

 

Ok i will look at all that next time i have it at the shop, But since today is friday it wont be for a few days.
ALSO i forgot to mention that in FL at night when the temp drops or we have a relatively cool day, it seems like the idle is BETTER, not completely smooth but indefinably not as noticeable. I'm fairly certain that im looking at MAP, temp sensor issue or maybe even O2s that is causing poor fuel injection control