We have had our Clearwater/Odessa head on ours for about 4 years now iirc. I just recently had a couple conversations about this. I am going to be lazy and cut and paste my comments from there.
Here's one
Cracked between cylinders 3 and 4? It is a relatively common problem only in the 00-01 years with the 0331 head. Some go forever without issue and some overheat once and die.
Our motor was at almost 260,00mi when it ingested water. We pulled the plugs and turned it over to pump the water out and cleaned the intake. It ran fine for almost a year after that and one day it started knocking and the motor blew. When it was disassembled it was cracked right where the 0331 heads notoriously crack.
When you rebuild your motor you want the stronger redesigned TUPY 0331 head. It has the letters TUPY stamped into the redesigned, stronger casting between the 3rd and 4th cylinder. They came on 02 or 03 4.o I6 motors from Wj or Tj Jeeps.
We did a new Jasper short block and wanted a new head without searching for the TUPY that would be used or rebuilt. We went with the Odessa/Clearwater Cylinder heads redesigned 0331. It can be had on E-bay with or without core charge.
This is also the moment you decide if you will ever want a stroker. For me with 4.56 gears and no desire for tires larger than 33" I decided the extra power wasn't worth the possibility of sacrificed reliability and longevity.
Another option is to switch to the earlier 0630 head You can search Naxja and find a couple of ways that it has been done. It is supposed to flow better and needs the earlier exhaust manifold.
Or use this exhaust adapter plate
http://www.naxja.org/forum/showthread.php?t=919384
You would also have to fab a little bracket for your coil rail.
I just went with the redesigned 0331 for simplicity.
Another one:
We got around 260k on ours and had no problems with the stock cooling. We ingested water in it one time, after pulling plugs and cranking it to pump out the water we cleaned the intake and ran it. The motor lasted us another year or so before it failed. I don't think we ever really overheated it but it did crack where they are prone to.
We have the Odessa/Clearwater redesigned 0331 on our new motor. We also keep it nice and cool with CSF HD 3row rad, Hood vents and Trans cooler/filter setup. It also has a cowl intake so we don't breathe in water again as well.
I hope something in there is useful lol. We haven't had any problems and I feel like we put some strain on it being that we have towed our trailer long distances and off road with our Xj.