I dug up my notes from when I installed a new head on a 2000 XJ 4.0 and have copied some of that info here. Hope it helps.

* Degrease all bolt holes and blow out with air
* If required install dowels for intake manifold in new head. Verify there are no rough edges or burs on the dowel pins.
* Check manifolds for flatness at sealing surface to head. Clean up carbon from around port openings. Mating surfaces must be clean and flat.
* Many rebuilt or new heads do not come with the exhaust manifold studs at each end of the head. They are also prone to breaking. Best to buy new (available from Chrysler dealer, p/n 6036193AA, 2 required). Alternately transfer from old to new. Requires external hex socket size E8 to easily remove (later years only). New studs have a thread sealant, probably because these may enter the water jacket.
* Install manifold gasket clean and dry – no sealant. Either side of gasket can face out if cutouts align. Be certain all surfaces are clean and free of carbon buildup or raised edges or dings.
* Clean up all head bolt holes with thread chaser (not a tap!) or old head bolt. Bolt should run in and out freely. This helps ensure proper torque later.
* Degrease all bolt holes and blow out with air
* Verify torque on manifold bolts
* Clean underside of head and block final time
* Fabricate guide pin from threaded rod or other bolt (can use head old head bolt but they are very hard). Slot top of guide to allow removal with screwdriver. Install cut bolt for guide
* Clean and oil cylinder walls & around circumference of piston
* Install head gasket, verify orientation
* Verify bolt #14 is in place and held above bottom of head with tape around top of bolt prior to installation
* Verify down pipe bolts removed and aligned
* Lightly oil head bolts and seat area on head if recommended by bolt manufacture
* Follow head bolt manufacture instructions or Factory Service Manual regarding lubricating head bolts or installing dry. For the Victor Reinz bolts I purchased lightly oil bolt thread and head per head bolt manufacture instructions. Reduced torque 5 ft-lb.
* FYI - Reference Victor Reinz head bolt installation instructions VRINST041 (says use oil): http://media.spicerparts.com/cfs/fil...store=original

* Add a small amount of thread sealant in head bolt hole #11 that goes thru water jacket. Loctite 592 or similar pipe sealant.
* Place a small amount of sealant in block hole only, not on bolt, to prevent sealant build up in head and under head of bolt.
* Follow torque procedure for head bolts. Proper torque is important.
* Don’t forget to reattach ground strap to the top of head bolt #14. Top nut is likely 15mm.

 

I've got the jeep running and it runs good. No coolant in the oil and no leaks, new problem though, transmission goes into gear and drives but it wont switch gears. Not even manually. I didnt drive this jeep before I bought it so i cant physically say it shifted but i bought it from a buddy of mine and he said he drove it up the road and back with the bad and it shifted fine for him. Only thing done to this jeep was the head replacement.

 

Not sure if this could cause your problem but check the transmission downshift cable that attaches to the throttle linkage.

 

Found a couple of photos of my 2000. The transmission kickdown cable is the one nearest to the front in the photo attached.

 

Closeup of attachments to throttle.

 

That last picture is the cleanest intake I have ever seen... what's up with that

 

The kick down is the first thing I checked and ok. I'm lost on it, I just dont know much about automatic transmissions, I'm sure it's something electrical because it dont slip and the fluid level is fine as well as the fluid itself, no metallic flake or anything.