I actually did a bunch of research on this. The 2.8 CRD diesel in the Liberty is a pretty decent engine. It is Italian made by VM Motori and is a pretty basic electronically controlled engine. I couldn't find any production parts to mate it to a Toyota 4 or 5 speed, so in my opinion, keep the Liberty gear box unless you have a full blown machine shop to build adapter plates and fly wheels from billet. The engine remained largely unchanged for the short time it was produced.
The other one mentioned was the 3.0 CRD, or OM642, in the Grand Cherokee. If I had my choice to put into a cruiser, it would be this one. Not quite the fuel sipper that the 2.8 is, it still garnered upper 20's (in my real life driving experience, not on paper). It is smoother than the 2.8 (I have driven both). And most importantly, it had way more power than the smaller Jeep. You will have the same challenges putting the 3.0 in as the 2.8 so why not go for the bigger smoother stronger? Pretty sure that is what my ex's were thinking.
Obviously there are pros and cons to both engines in terms of availability and cost, as well as the rebuild issue that was mentioned (I never looked into that aspect). But if properly maintained, these engines should last a very long time. I was quite impressed with MB's testing of this engine in their e-series cars. Wish I could find the link for it.
Good luck and let us know if you do this swap. I would love to see it done.