I did quite a bit of research and waited until I had all parts in hand before starting the swap. It took about two months to get everything. I would recommend paying close attention to my spreadsheet because , while not perfect, there are several things on there that are not listed on the JSS BOM sheet that you will need that may cause you a WTF moment along the way. Such as the hump coupler that goes in between the air filter and throttle body. In the time I was waiting I did research and had a couple guys from the forum lined up to answer questions. Do this! JSS is a small understaffed outfit so be prepared to wait for answers you could get from a forum member. There are a shitpile of videos on YouTube that you can get good info from even if it is not necessarily relative to the subject of the video. While I am thinking, I would highly recommend baggies and sharpie to keep track of parts removed. Also take pictures for future reference. Also this thread is not to be anything but helpful to anyone,especially those like me, with little to no mechanical experience.
This swap can be achieved with a basic set of hand tools, wrenches, ratchets and sockets. A 10mm, 13mm, 15mm and an 18mm will get you pretty far. Specialty tools needed: angle grinder, Dremel, Die Grinder useful, fuel line disconnect tool, a pipe cutter also valuable but not imperative. Large screwdriver or pry bar. And a welder or person that can weld. Engine hoist or a lift. And believe it or not a long weekend.
I took the body off approach, which having done it that way, is the only way. Obviously it can be done body on. Motech has a couple of good videos regarding preparation of body for removal on YouTube. May take a couple hours. The body was removed and replaced without opening the brake/ABS system. Simply unbolt the Master Cylinder from booster. For body replacement you will need to remove the tray on which the ABS module and PCM mount. Once body is back on you can slide the tray under everything. When body was removed we just set it on a utility trailer and parked it under a shed. Once the body was removed that is when I removed the radiator and all that shit.
Pic to how I secured ABS without opening and taking body off.
http://www.jk-forum.com/forums/attachment.php?attachmentid=643092&d=1460051166
TIP. If you remove body. Use a plumb bob to help realign. The two studs on the front of the body if aligned will pretty much guarantee the rest will jive.
PREPARING THE MOTOR.
I would recommend holding on to the 3.8 because, in my case and likely yours, there will be a few parts to save. Like maybe an AC line, fuel return line, Evan canister, power steering pump or the fittings and the rubber transmission mount. JK pump can be used but in my case it appeared the pulley was going to hit Steering box. If it works for you drill out the mounting threads. I used the Hemi pump with smaller pulley and removed the fittings fro JK pump. I had to trash the pulley on JK pump to get fittings. The elbow can be removed by carefully twisting back and forth with and adjustable wrench. The brass fitting is 7/8", I believe.
Fittings needed from JK POwer Steering Pump
http://www.jk-forum.com/forums/attachment.php?attachmentid=643096&d=1460053467
VIDEO: POWER STEERING PUMP
EXHAUST MANIFOLDS. East coasters be prepared to replace exhaust manifold studs, especially the doubles. Two broke off for me. Consider PB Blaster a while before attempting to remove.
EXHAUST: as I said before I am using two stock JK cats with no issues at all. And I will until they don't perform any longer. As far as O2 sensors go, you can definitely use the stock downstream/rear sensor. I know of someone using all stock JK sensors with no issues. I ordered 2 new O2 sensors as listed on the spreadsheet.
The CAPACITOR mounts on the aft end of the drivers side head. It will be obvious where it goes. And don't forget your two grounds on the rear of the heads.
WIRING HARNESS. The wiring harness is easy. Find a component or two that you are certain what it is and start there. The rest will kind of let you know where it goes. Length dictates.
NOTE: Apparently there are two different types of connector/harness patterns for the Intake Air Temp Sensor. So you may want to figure out which you have so they can make it to use your JK sensor or you can just get another for $15 off beat. If not they just kind of guess which you have.
Difference in harness patterns
http://www.jk-forum.com/forums/attachment.php?attachmentid=642636&d=1459690915
NOTE: Also there are a couple different types of THROTTLE BODIES. First type is 2012 and below with an 85mm bore it appears, with a part code of 53032801AC, 6 pin (3 pin wide)harness. The second, 2013 and newer, with a part number of 53034251AB which I believe is an 87mm bore Throttle body. It has a single row harness 6 pins wide.
Newer Throttle Body
http://www.jk-forum.com/forums/attachment.php?attachmentid=642635&d=1459690279
It will be necessary to repin the C3 harness that will remain attached to body. HOTWIRE AUTO has a great set of instructions for this procedure.
Repinning Instructions
http://www.jk-forum.com/forums/attachment.php?attachmentid=644345&d=1461160730
FAN and CLUTCH If you use the 18" fan it will hit some accessories. So once the fan and clutch are installed just bend the blades back a 1/4". Also on the intake manifold there is a point that sticks out towards the front about an 1.5". Cut it off.
BATTERY/STARTER CABLES. You will at least need to extend the ground or you could make some about 12-18" longer.
That's all I can think of on the engine.
OIL FILTER ADAPTER. After removing the old oil filter stud buy welding a nut or I swear it could be removed with a gigantic Allen wrench. When installing the new adapter make sure the new gasket it not twisted offset. And just bolt on. It may seem like it will be in the way looking ahead but it all will fit. TERAFLEX GUYS WITH FRAME BRACE. Have a bend put it to clear the adapter or just leave brace bar off. I spoke to Dennis about this.
You may end up with two oil sensors. I left both and use one. Taped off the one not in use
NOTE: I have heard of an instance where a guy upgraded to a front Dana 60 and there were potential clearance issues. I believe he ended up doing a remote oil filter setup. I do not know how much lift he had.
BATTERY TRAY/BOX . Fairly straight forward. One wire bundle will kind of be around the top and one will be under the tray. Rubicon guys, the locker relays that are in the back passenger corner of the battery tray will likely need to be repositioned to the top of the passenger side fender just a few inches forward from its original position.
My battery ended up being in the rearward position due to short cables with negative side toward pass fender. Make sure you trim the stands at the firewall.
NOTE. when installing the TIPM to the new mount and have to remove any of the harnesses. Make sure you use care releasing the locks as they may be brittle. And also label which ones are which. I stared at some pics quite a while getting them in order. The Air Filter adapter will ATTACH TO THE BATTERY BOX so before bolting the TIPM mount to the battery tray, bolt the AIR FILTER ADAPTER to the battery box.
BATTERY TRAY INSTALL
AIR FILTER ADAPTER: I would recommend bolting the air filter adapter prior to mounting the TIPM for accessibility issues. I Persoanlly tightened it to where I could still, with a bit of force, adjust the position a bit. The air filter is a tight fit. Be sure to install the hump hose and T-clamps in between the Throttle Body and Air Filter Adapter.