Jeep Strokers

Newbie here with hopes that the stroker guys can guide me right...
I have a mutt, actually 2, that I had to pull the head the other night. It's a 99 with a 89 Renix longblock /2686 head. I did the swap last November after my #5 cylinder popped a wrist pin and demolished the piston. I ended up with that platform only because a friend had it so I could pay later. When he bought the complete engine I was there and the guy stated it was freshened up to swap out a 4 banger. Once I got the motor I pulled valve cover and saw fresh valve seals and a new fulcrum on #6 so I felt confident to not pull the head or put freeze plugs. My OCD took over and I pulled the pan and what not to clean and paint while putting rear main timing chain set etc. Now months later I swap ac compressor to get the air working again, it's hot in fl, it starts overheating on my girl intermittently. She is using for DD for new cleaning business. I replaced thermostat checked belt and ran for hour in drive with ac on high with no problems. Long story short this went on for 2 weeks messing with but still driving daily. Eventually the head gasket popped last week. Oil never got in the coolant, I was watching for that every time she said it got hot.
I'm fairly proficient with the 4.0 and pulled the head in a few hours the other night. I found what could have been the catalyst. Whomever put head on put sealant in head bolts causing it to get on mating surfaces. Also my water jackets were full of rust, I think from keeping coolant flush and my terrible city water in it for months. That is probably why the middle cylinders got so hot it melted the plastic cover for wiring that goes on middle bolt. Looking at the domes to me something doesn't seem right
The next kicker is the pistons are not coming to the top of the block and major carbon build up
I'm in a major time crunch to get back on the road but I can't live with myself if I don't correct something if I'm able to. I'm about to port match the intake gasket, 99 intake, clean it up best I can since the local machine shop turn around isn't quick enough. I noticed the exhaust ports are larger than my exhaust, 99 manifold, so I'm wondering if I should fill them since typically the port is smaller than exhaust. Then polish to alleviate carbon. Would I be wrong top do so? I appreciate all the input I get. Also if anyone has questions about the longblock swap feel free to ask since I learned by mistakes and brainstorming already. The XJ ran great up till this and didn't have any typical lifter noise etc. I have my original motor on a stand waiting to be stroked but I need this one to get me buy for who knows how long. Thanx ahead of time

Wow, lots of information in your post but I am having a hard time digesting what your asking. Could you respond with a simpler format ? I am old and senile and can only understand one thing at a time.
What am I looking at in the pictures ? A Renix 4.0 with a ? Casting number head ?

Sealant is used on #11 head bolt because it passes through the water jacket. None needed on the rest.

1. Question one
2. question two
and so on.

jsawduste wrote:Wow, lots of information in your post but I am having a hard time digesting what your asking. Could you respond with a simpler format ? I am old and senile and can only understand one thing at a time.
What am I looking at in the pictures ? A Renix 4.0 with a ? Casting number head ?

Sealant is used on #11 head bolt because it passes through the water jacket. None needed on the rest.

1. Question one
2. question two
and so on.

The head is a 2686 casting and every head bolt had sealant.
1. Does the unusual colored build up on the domes look right.
2. Is it worthwhile to only match port intake since I can't get it to machine shop.
3. Is it safe to polish domes without disassembling head?
4. Exhaust ports are larger than exhaust should I fill and polish what I can to help prevent excessive carbon build up again.
5. The piston are not reaching top of block consistently on all cylinders. Is this a sign of anything.

First time having the head off a Renix 4.0 so doesn't appear the same as other ones I've had apart. Could thks have after market pistons.