I don't hear a lot of great stuff about JTO, but I suspect the kits are all the same. As long as they have koyo bearings, you are OK. I got my kit from Mudrak, but I'm sure Kurt would have the right one too.
The shim pack is a tough one. When I did mine, the preload was wrong, and so I had to re-shim. There is no way to measure, so you shim, measure, pull apart, reshim etc. It took me 3 tries to get it right, which means you will probably need to have a full pack to start. The shims are $7 each and there are 10 or so of them.
If I were doing it again, I would use the same kit, but I would use all Toyota paper gaskets, especially the middle one where the case splits and the one on the rear output cover. The total thickness of these changes the preload when it goes back together, so it makes sense to use the factory gaskets and lower the chance the preload will be wrong. It also makes sense to use a factory rear output seal.
If you have the whole thing apart, there is no reason not to replace ALL the bearings. Not replacing one set sounds like doing the job half way.