I ordered an Atlas 2 speed transfer case and the 6L80e adapter (#50-9600) from Advance Adapters.
I decided on a 3:1 ratio to go with the deep gearing of the 6L80e. As seen by the engine this will be roughly similar gearing as a 4:1 transfer case behind the stock TJ or the 4L70 transmission. If I later decide that it's not enough gear the Atlas can be regeared to a different ratio.
For the rear yoke I'm switching to a 1350 joint. This will be stronger than the current 1310 and will better put up with shock loading when getting rowdy with the V8. In the front I'm likely still going to be running a 1.25" driveshaft to clear the transmission and engine and the smallest 1350 driveshaft Tom Woods makes is 2" diameter so I'll be sticking with the 1310 joint up front. Once I get everything in, if I find that I can run a 2" shaft I'll switch the yoke out to 1350.
For the tailhousing there were multiple pros and cons of each choice. Since my engine and transmission computers do not understand what low range is, the computers can not correct the dash speedo when in low range. The GM VSS tailhousing could be used for the dash gauge so it'd always report the correct speed but I can't remember a time that I've looked at what speed I'm going while in low range so I think it'd add unnecessary cost and wiring (although not hard to do if your OCD requires a correct dash speedo). There's also the "standard tailhousing" which allows for the use of a Jeep speedo which could be useful if I were retaining the stock Jeep dash. Since I didn't see a benefit in either of those I decided on the short tailhousing which is cheaper and 2" shorter than the standard tailhousing. With the 4L-series transmissions I'm pretty sure having the GM VSS tailhousing is required.
I also specced the case with a sight tube, 4wd switch, and low range switch (although I'm not positive I'll be using these switches yet. As an experienced Jeeper I can't think of a reason to keep the 4wd light on the dash since it'd be pretty obvious if the transfer case didn't go into 4wd or if I forgot to take it out of 4wd on the street?). If I decide that I want a different shift table for low range I can use the low range switch to trigger the 6L80e's tow/haul mode and put my low range table in there.
I decided on a 3:1 ratio to go with the deep gearing of the 6L80e. As seen by the engine this will be roughly similar gearing as a 4:1 transfer case behind the stock TJ or the 4L70 transmission. If I later decide that it's not enough gear the Atlas can be regeared to a different ratio.
For the rear yoke I'm switching to a 1350 joint. This will be stronger than the current 1310 and will better put up with shock loading when getting rowdy with the V8. In the front I'm likely still going to be running a 1.25" driveshaft to clear the transmission and engine and the smallest 1350 driveshaft Tom Woods makes is 2" diameter so I'll be sticking with the 1310 joint up front. Once I get everything in, if I find that I can run a 2" shaft I'll switch the yoke out to 1350.
For the tailhousing there were multiple pros and cons of each choice. Since my engine and transmission computers do not understand what low range is, the computers can not correct the dash speedo when in low range. The GM VSS tailhousing could be used for the dash gauge so it'd always report the correct speed but I can't remember a time that I've looked at what speed I'm going while in low range so I think it'd add unnecessary cost and wiring (although not hard to do if your OCD requires a correct dash speedo). There's also the "standard tailhousing" which allows for the use of a Jeep speedo which could be useful if I were retaining the stock Jeep dash. Since I didn't see a benefit in either of those I decided on the short tailhousing which is cheaper and 2" shorter than the standard tailhousing. With the 4L-series transmissions I'm pretty sure having the GM VSS tailhousing is required.
I also specced the case with a sight tube, 4wd switch, and low range switch (although I'm not positive I'll be using these switches yet. As an experienced Jeeper I can't think of a reason to keep the 4wd light on the dash since it'd be pretty obvious if the transfer case didn't go into 4wd or if I forgot to take it out of 4wd on the street?). If I decide that I want a different shift table for low range I can use the low range switch to trigger the 6L80e's tow/haul mode and put my low range table in there.