I have a 04 jaguar with a 06 engine it, i have a lean code but replaced everything for that and car jerks once in awhile?

You checked for vacuum leaks around the intake manifold mating surface to the head then?

yes and when i took it to a authorized jaguar dealer they gave me a 1,000 for testing bill and said they don't know what it is. the car runs flawless but has this engine light and every once in awhile when i try to press the pedal the car will lag then kick on me but when i let go of the pedal and re-press the pedal the car will take off up 80 with no problem and run great. its a 06 engine in a 04 jaguar 3.0 awd. resealed all wires becasuse before i would have engine system faulure and gearbox default but i have resealed everything and havent had that problem since. Im thinking its the cars computer glitching once in awhile with this new engine, but im 100% sure.

You think the dealer would know of any differences between the two years on the computer thing, not sure, otherwise motor running good, not thinking it would be the computer, almost sounds like some condensation in the gas. Try putting some (and I can't spell this) isysoprofel in a tank or two of gas like the RED bottle of Heat. Not a methanol additive. (yellow bottle heat)

New gas tanks as well as fuel pump and transfer pump between tanks, got fuel pressure and trims where they need to be, i will also notice my ac settings will change every time i start the car the ac wont be on the last setting set, also windows somtimes dont roll up Automatically and car will somtimes refuse to lock but the horn will beep, the car runs great no signs of anything wrong mecaniically seems to be electronic problems thats why im thinking its the computer not being able to handle the new engine it because it was programed with the old engine. I really dont want to junk this car it was a gift from my father i wanna keep It forever.

Don't ever junk that car, keeping the car has fond memories for you, keep at it, good learning experience, memories and learning are good things... I don't think the computer (ecm) is the problem at this time, but there should be a Body Control Module under the car somewhere that could cause these symptoms you now describe. Just so you know I don't know Jaguar at all but I am a trouble shooter, I know systems, causes, and such for a vehicle to operate properly. So on a car like that, probably a finicky one. You have all new fuel system up to the engine, how much fuel have you put threw it since it all installed? Don't know if you are but I would run premium fuel with a isysoprofell base in it, (I haven't learned how to spell that yet, but not the methanol base one). I am thinking with all that new, there is bound to be some condensation. I hope this helps, gotta be something simple since it has ben checked out pretty thurrally.

Isysoprofell would be in the gas additive to break down any water caused by condensation or gas.

Tried that and fuel cleaners i only run premium gas, new throttle body and sensors for gas pedals, everything fuel wise is good, fuel pressure and such, i would love to keep the car but i need a car badly ive had this car in the shop for just about a year now all tech lines give up on me and all these experts that come and look at the car end up being helpless i really need to get this resolved.