Big Job, my 89 YJ had the same problem when I bought it. I did not know if it was a blown gasket, warped manifold, or broken stud until I pulled everything apart. Since I found new exhaust manifolds on ebay were only $25 I ordered a new manifold, bought a gasket at Kragen and started the job on a Friday so I would have plenty of time if I needed it. Some of the bolts hold both the intake & exhaust. 1st I had to pull the throttle body and inake plus drain some coolant, then the exhaust manifold was ready to pull. Turned out it had no gasket on the exhaust manifold and the 2 studs were badly damaged preventing the nuts from tightening down all the way. I was able pull the studs & fix them with a tap & die kit. I then installed the new exhaust manifold & gasket but getting a torque wrench on some of them is really impossible. It has been running great since I finished the job which did take me 2 full days of back-breaking work and lots of WD40! Good idea to clean all the bolt holes with a tap while you have it torn down. Also the EGR tube was a real pain to transfer to the new manifold.
