New member here.

And new Jeep owner (’89 Pioneer). My Jeep came to me with all kinds of driveline issues and a well-abused hitch receiver on the back, so I’ve also been looking into rebuilding the 6 sometime in the future. I haven’t had the rig long enough to do a leakdown, but it’s sort of a moot point at the moment because I bought it with a blown head gasket.
I agree with doing a simple engine swap if you can. Personally I plan on buying a core engine, building it, and swapping it into the Jeep. This way I still have the Jeep driveable, and of course a mule for trips to the machine shop.
Anyhoo.
In my experience, it is not feasible to do an in-car rebuild. This is how I attempted my first build and it was a disaster. And it was a lot of climbing around the car and other assorted time-wasters.
There are engines designed for in-chassis rebuilds, but this is not one of them. If space is a concern, which it is for most of us probably, if you have space to keep the Jeep parked for a few weeks then you probably have space to rebuild the engine. It just requires more improvisation. Not to mention, most of the time the engine is out of the chassis it will be at a machine shop.
I have not rebuild a 4.0L Jeep, but I have rebuilt 30+ Honda engines and a few dozen from a few Japanese and German makes. I have done a lot of flow work, blueprinting, and examined a lot of blown engines. ASSuming this knowledge carries over to the Jeep, this is how I will do it:
Master rebuild kit, preferably with forged pistons. (It’s not a strength thing, it’s a heat thing. Forged pistons move heat more quickly than cast, so they can take more of a thermal as well as mechanical beating.)
Cylinders will be overbored as little as the condition of the bores will allow. I suspect 0.010” over shall do, but haven’t seen pistons smaller than 0.020” over. Shouldn’t be a problem either way.
Not going to turn the crank journals down. This weakens them unnecessarily, and they shouldn’t be scored that deep anyway. Polish only. However, my experience is 100% in nitrided forged steel cranks. A stock Honda crank is happy at 1,000 hp. I’m very curious to see what the Jeep crank looks like.
Still researching the rods – would strongly prefer an aftermarket rod with separate cap bolts. Several reasons for this. One of them is cost – prepping stock rods can cost nearly as much as a set of new performance rods. Also, if the stock rods use pressed-in wrist pins, they won’t be compatible with a forged piston. It’s “possible” to convert a pressed-pin rod to use a floating pin but it’s a pain in the butt to machine the rod this way.
For the head, I plan on doing a pocket port and using new stock INTAKE valves and aftermarket stainless EXHAUST valves. Why? In a word: Flow. I have never once seen an off-the-shelf aftermarket valve flow better than a stock valve. Stock intake valves tend to be a two-piece affair (stainless head welded to carbon steel stem, then ground and polished). Fine. They do this for wear characteristics. Flow is less of a concern on the exhaust side, and stainless valves will have a higher heat handling capacity before they burn. Just a safety measure for pounding hard on sandy Mojave trails.
Then I plan on boring/reaming out the stock valve guides and pressing in new bronze guides. Just a wear issue. If you cannot or will not use bronze guides, skip the full stainless valves and stick with stock. The stainless valves are not really compatible with stock iron valve guides (wear issue). I’ll cut the valve seats cut to stock angles, then shim springs to correct installed height. Then surface the head so the deck is true to the datum point.
As for block machining, I will probably draw the line at surfacing the deck true to datum, and of course boring/honing the cylinders. In my experience line-honing the main caps doesn’t really help you with anything (they’re always true).
I haven’t selected a camshaft yet; need to do more research. If you plan on swapping to a non-stock cam I would consider mock-assembling the engine to measure piston-to-valve clearance before final assembly. This step adds a few hours to the job but in my opinion is well worth it.
Depending on piston-to-valve I may deck the engine further to reach .045” piston-to-head clearance. There are reasons for this…. Anybody care to add to this thread with reasons why?? ;-)