Hey jrod , welcome to Jeepz.com :welcome:hoping for someone who has experience with actual swaps from different years 4.0 I6 engines to post their experience , but will offer what I have found . The first thing I want to say is that , as you may know , the best source for this info is a recycler since they have the HOLLANDER EXCHANGE catalogue for interchange between year, make and model of various salvage parts . Years ago when I worked in the auto wrecking business , we swore by the "HOLLANDER" as our bible. Experience taught us that staying in the GM , FORD , CHRYSLER , etc. family was the start and engine size and weight class thereafter for most interchange compatibility . I decided however to look at QUADRATECH, and research replacement engines for compatibility . It is too specific to post , but I invite you to check their listings for good info that will help you know what year and what model jeep is best to find an engine from. Off the top of my head , I will say that I recall something about '99-'01 4.0 liter engines with cylinder head casting # 0331 in their serials having a production defect necessitating cylinder head replacement . I don't think you want the extra work or gamble with a used engine with this issue for example.
It will be necessary to research application as what I have found so far is most year XJ and zj I6 4.0 swaps but not YJ. Needs to be researched to confirm exact. Motor mounts vary year and body but Chrysler family I6 bell housing bolt pattern should have been retained , leaving the crank pattern and diameter to be questioned for flywheel , for example. Later engines used cam position sensors in place of distributors , but should swap ? Accessory bolt pattern such as a/c & alternator , power steering , etc. are to be questioned per application which is why block and cylinder head casting numbers are of value to this swap as you want the most painless parts swapping possible . Less time and money spent the better. There are more items to consider if we really think about it such as fuel pressure volume ( 4 cyl to 6 cyl + 2 injectors) , for example .
One major item of importance is the PCM and engine wiring harness since you cannot reuse your old ones for a I6 swap . I wish not to deter you and have you limit yourself to a 2.5 , I think a 4.0 is a great idea but all else must agree such as a 5-speed ax15 in place of the ax5 that is most likely in place now. Before lifting a wrench , please check what items you currently have that will be of swap concern such as drivetrain and engine accessories and possibly compare to a 4.0 YJ or XJ or even a zj since we don't know where your donor engine will come from . Hope this helps , I'm sure there is more but I know you got to start somewhere and member contribution will help out as it is certain that other forum members have encountered this very swap before !
Also, check our website for related threads on same or similar questions as yours . That is a good place to start ! Wishing best of luck , Greg