Follow the link in my sig to my tdi yj in progress.
I'm using all toy driveline but it can be done with the same acme adapter I used if you source an input shaft and bell housing from a Toyota. The jeep and Toyota tran's are the same core unit... Unless you have one of the old Peugeot trans's in yours.
There are builds out there... Search tdiclub, pirate, jeepforum,etc. pay attention to the toyota guys... Most of the info that has helped me came from 4runner and truck swaps... They are pretty common. Just be prepared to touch every system on your vehicle... Mounting the engine is the easy part... Finding fittings and plugging it all together to make it work is the challenge.