Wow, it's been too long since I've visited this thread. I didn't know there were cool plans going down up in herr.
As far as emissions, it shouldn't be too bad of a problem. I don't know of any OBD2 ZE's, since the Probe guys don't care about that shizzle. Best bet for getting an OBD2 KL is the 98-02 626, since it's already the KLG4 with the lightweight crank (over 10lbs lighter). The other good OBD2, and also a low stressed motor is the Millenia, since they were all auto. DO NOT get the 2.3 Miller supercharged motor. It's not the same, and is a huge heap of crap. The problem with getting the regular KLDE from the 626/PGT/MX6 is that the sensors were different for the different years: 93-94 had OBD1, 95 had its own specific stuff, and 96-97 (before they got discontinued in the case of the PGT and MX6, or changed body style for the 626) was OBD2.
Anyway, if you're going to do the ZE, it should still be fine. I've heard that they can pass emissions, even in Cali, which has the strictest stuff, AFAIK. Do you have a visual inspection, Evan? There's absolutely no way that they'll be able to tell what kind of KL it is (even with a different intake mani, there are just too many, and emissions workers are usually ruhtards). Just tell them it's from an 02 626, and the 'older motor' should not be a problem at all.

If you still have trouble getting the ZE to pass emissions, you can get a different intake mani that has an EGR port, such as the G4 or the Milly one, but I'm not sure about which ports match up to which ones. The DE has oval ports, the ZE has square ports, and I think the Milly has oval port holes while the insides of the runners are square, so... it gets confusing quick!
Phen, as far as the axles, if they're the same as the FS 626 (I wouldn't expect them to be), they're good up to like 250whp or something, so even though the v6 ones are beefier, they're not needed, at least until he turbos the KL..
Also, Evan, that motor you posted doesn't come with a ZE, or any, ECU, and that's a biiiig must-have. If you run a regular DE ECU, it won't be making the power of the ZE, and that's the whole point of having one!
I think I'm up to 3 informative posts, now!