Installing the Engine
My general installation consisted of pulling the 4.0L and I actually left the transmission in place. I left it in because the 4.0 wasn't bad to pull and I wanted to measure off the face to check the engine mount placement. Honestly I'm not sure this helped me.
However pulling the R2.8 with adapter from the transmission was rather time consuming. I bolted on the adapter, leaving off the clutch to check motor mount placement, but couldn't get the frame motor mounts in place like I hoped and after pulling the R2.8 after that first fitment, decided to scrap the extra test fit.
I should have pulled the trans here, separated it outside of the vehicle, install the clutch, and bolt the trans ans engine easily and attached the motor mounts, add a new trans mount. Then install everything and get it situated, protected the engine/Jeep and tack welded the mounts and pulled everything back out.
That's what I should have done, but I didn't and you really don't have to. The Axis Motor mounts only fit one way basically. However there's a little wiggle room. I should have measured from the most forward part of the control arm bracket to 1 in to the engine mount, but again I screwed up a bit and the mounts were 1/8" forward. I was able to make that work without any real issues, but it did take some fitting. However, when routing between the firewall and engine, I'll take every fraction of an inch I can have. The issue is DOC clearance, if my DOC hit anything, I really wouldn't care and would modify it to fit or remove it.
Ultimately I have about 1/4" of clearance, but possibly a bit less with the DOC and upper control arm bracket. Looking back I was just kind of droning from working too many hours in too much heat, with too little rest. My MIG had failed and having the most experience with TIG, was going to TIG the vertical parts, but it wouldn't go about 70 amps, I found out later why, but I only had stick available and I have the least experience with stick. I think the welder issues distracted me as well. All the welders at the shop I work at were out at customer's facilities, so I was on my own and pushed on.
I did catch some old wiring insulation on fire which was fun, I'm so used to welding on a bench that it's amazing how much you can suck when your position changes. The welds don't look good, but they should hold. As a note, I painted everything with a light color paint and taped them off for the black paint so I have some contrast to keep an eye on them.
A couple items I didn't have at the time that I highly suggest installing before the engine is installed is the aftermarket oil pressure sensor, and the block heater. Block heater is pretty easy, but the oil pressure sensor, caused me another colossal screw-up later.
I did make a couple of decisions and exchanged some etorx bolts for hex head on the Cummins starter and allen head for the AX-15 top bolts and made an access port for the allen bolts on the trans.
Once the engine was in the only issues were mainly routing everything and trying to keep stuff clear and keeping track of engine, frame, body, suspension type stuff and how everything needs a bit of give and clearance. Ie where's my heat source, add some insulation and where am I going to secure this part.
Another screw up, but not a bad time to address it was the heater core. I damaged a heater core tube when trying to remove a heater core hose. It pissed me off at the time, but really it was pretty easy to swap out with the dash being mostly pulled already and battery and PCM removed.
Anyway, while routing everything I decided to add a 1" body lift. In my head I was thinking the tank went with the tub, which was a major bonus to me as I've hit my gas tank several times in the past. I was wrong, but this was still useful later on. Technically I could make room and move it up an inch, but decided not to unless it is a problem in the future. I mainly only hit when running 31" or smaller tires.
I found my brake lines fairly rusty, steering gearbox had been leaking, the tcase had water in it, a rear track bar bushing was worn out, a brake bleeder was seized up, and my fuel tank fill bezel was broken. I replaced all that stuff at the same time.