You can read below from someone who claims to have done the swap. If you believe him, I don't.
He claims it does not matter what position the CPS is on the flywheel.
Apparently there is a 3 wire CPS that will fit.
Apparently you have to use the Mopar 05-06 master/slave. I suspect the slave has a different travel length.
He makes no mention of drive shafts, the 6 speed looks longer, you may lose your front and rear DS.
As I suspected, the shift tower is not in the same position, you will lose your console, if you have one, you'll have to modify your tunnel, regardless.
I found them on Ebay for around $900, assuming you get one complete, parts are expensive, poster is correct, shift towers are $700 to $1000 depending on part number. Go to Quadratech and look at part pricing, bell is over $1000.
New clutch, new slave/master, CPS, wiring connectors.........etc.......possibly new DSs.......this is a minimum $2000 swap. Trans mount alone is $85 and surely you will have to modify your x-member. You'll possibly have to modify your TC linkage or go cable.......if cable, add another $170.
And, you have to believe that you can make it work.
Parts are NOT plentiful, I found a thread where a Mopar dealer had posted Chrysler delivery totals year to year, there was something like 91 6 speeds ordered in 2012.
One of the articles I posted stated what I already knew, new trucks are not even being offered with manuals, future factory support will soon dwindle.
My comment about your 'buddy'- When my last trans went out I planned on having it rebuilt, there is not a competent Jeep manual rebuilder near me, Charlotte, Nashville, or Atlanta, those were/are my options. Finding a good manual shop is becoming more and more difficult.
http://www.wranglerforum.com/f19/6-speed-nsg-370-a-31284.html
Do not purchase a harmonic balance or even call the guys that make these for advice. They did not help me, but only made things confusing. USE YOUR EXISTING FLYWHEEL!!! Do not buy another one. It is not necessary! Don't worry about the position being different on the new transmission. The crank position sensor just tells the engine that a piston is at top dead center and is used to time the spark plug firing. You have six pistons, so it doesn't matter which one is in the TDC position. The only trick is getting the 3 CPS wires correctly connected. They are not in the same order as the old ones. You will need to test them 123, 132, 213, 231, 312 and 321. I think the middle wire was left the same position. One of those 6 combinations is correct and your Jeep will start. The others will not work and your Jeep will not start. It is easy to diagnose. Remove the wires from the old plastic connector housing. You can remove the metal clips from the housing with a special tool or something sharp. I suggest buying some tools for crimping and working with wire connectors (search: pin extractor tool). You can purchase these from Circuit Specialists, Inc, DigiKey Corporation - Electronic Components Distributor or Mouser Electronics - Electronic Components Distributor Here is the bill of materials (BOM):I found the wiring part numbers form another poster and purchased them. In the end, I used the Mercedesmetal pin connectors and removed from wire that they were attached to. Note: removing the crimped-on metal pins from the wires was really difficult, but I only found them sold with short wires attached. I used a 2 sets of small pliers to bend the crimps open. The Mercedes pins, clips or metal connectors (whatever you'd like to call them) were then crimped onto my Jeep's existing wires. This allowed me to put the new plastic housings (to make a complete electrical connector) without any goofy splices. This will keep your Jeep reliable and is really important to do correctly.Google the part numbers. The Mopar ones can be found on eBay.Mercedes short wire connectors (pins): 000-540-38-05 get 5Mercedes connector housing (bushing) for reverse switch: 168-545-27-28 get 1MOPAR connector housing 3 –wire pigtail for crank position sensor - CPS (same as the speedometer connector): 50-14-007AB $40.97MOPAR Crank Position Sensor (bolts to transmission bell housing): 04727451AATransmission mount bolts 10mm x 1.50 x 30mm – get 4 from Lowes or McMaster Carr2005-2006 center console – get 1 from eBay or existing consoleClutch slave cylinder: 2005-2006 Jeep master and slave cylinders (sold already assembled)My NSG370 transmission was missing the small rubber boot on the shifter. Mopar sells the shift tower with the boot only. It is $700, so I used a CV dust boot and later found one on eBay.Shifter Lever from NSG370Interior shifter boot - 2005-2006 Jeep: you will need to modify/cut off flange on bottom and drill some new holes in transmission tunnel. You could modify your old steel plate that bolts to the transmission tunnel, but it is a pain.Transmission Specs for comparison AX-53.93/2.33/1.45/1.00/0.85 with 4.74 reverseAX-153.83/2.33/1.44/1.00/0.79 with 4.22 reverseNV35504.04/2.33/1.38/1.00/0.78 with 3.75 reverseNSG3704.46/2.61/1.72/1.25/1.00/0.84 with 4.06 reverse