Steve Friend on the Jeep-L list on yahoo is doing this swap right now. Here is a link to some clearance issues, even with a modified pan:
http://www.jeepshots.com/users/sf/JeepMod/
"I am back to not having any clearance to the drive shaft again. The
clocking ring did it's thing in getting the Tcase out of the way and moved
the drive shaft out away from the pan, but it also moved it up and I only
have about 1/4" clearance. I am hating this project.
I have a call into Tom Woods to see what he thinks.
SF (made myself a two wheel drive rock crawler!)"
A reply to an earlier post about the differences in the tranny's:
"The TF999 is the lighter duty of the two trannys, The cases are the same between the TF727 and the TF999 But the pan is slightly different to clear the front driveshaft's on wranglers and cjs.
The TF727 was used in Wagoner's and full size jeeps for a couple of reasons. One, you didn't have the clearance issues you did in the wranglers because they are full width. Two, Much heavier then a wrangler so they needed a medium duty tranny to handle the V8 horsepower and the weight of the fullsizes.
Think of it this way, in the Chevy word the TF999 is made for cars or 1/4 ton vehicles, The TF727 is made for trucks or 1/2 ton and up vehicles."
And here is another post:
"The 999 and 727 are Mopar trannies which Jeep 'borrowed' and the internals are identical to their Mopar brethren. Save for the portion of the case that bolts to the engine and the output shaft and tailhousing adapter (in most cases), they're externally identical as well, so the pans are not CJ/Wrangler specific. The 999 is a medium duty trans based on the 904 and was used in 6 bangers on up to small V8's...the version used in Jeeps is a low gear version similar to the Chrysler 5th Ave 318 V8 version used in the 80's. The 727 is heavy duty and obviously physically larger and beefier. The 999 is plenty for a mildly built rig, just keep the TV linkage properly adjusted, keep it cool, and put a real vent on it if you're going to run it through mud or water."
I also did the tf727/dana300 swap in my CJ7, but I was running about 9" of suspension lift, so clearnce wasn't an issue for me.
Another site to look at is here:
http://www.jeeptech.com/convtrans/conv727.html
Hope this helps!
Jack