Its not a big deal which generation of 1JZ-GTE you have, unlike what was previously thought. Just get a new 2JZ-GTE PCV valve from the Toyota dealer before you run the motor, and the first gen motors affected by the PCV recall are otherwise identical to the 2nd gen.
Now, that's speaking strictly of the earlier twin turbo 1JZ-GTE, not the VVTi single turbo 1JZ that replaced it in 97, which is a bona-fide clusterfuck to integrate into any US car as awesome as the VVTi's potential may be.
A good check of the motor is to just pull the valve covers off. Most JDM motors have a very dark patina because they don't frequently go for long drives and thus that varnish likes to build up in the cylinder head. Don't try to clean it out or anything like that if the head is still attached - it'll break all that crap loose and leave it floating around in your oil. If it bothers you that much, just pull the head and have it vatted at a local machine shop.
As for the oil pan clearance issues you're worried about, keep in mind that JZ engines came with either a front sump or mid/rear sump oil pan depending on the vehicle it was installed in. Chaser & Aristo motors were front sump, and Supra & Soarer engines were mid sump. If one doesn't easily fit where you want it, you might look for the other, depending on whether or not your motorset came from a Supra, Chaser, or Soarer. Front sump pans are very cheap because they come on Aristo 2JZ-GTE's that people remove to install into Supras and SC's here stateside. Midsump pans are harder to come by because they are needed for the same swap. If you're on a budget I'd look for an SC300 in your local u-pull-it and steal the upper and lower oil pans from that engine, as the upper pan's cast nature allows you to drill and tap it in the proper spot for oil recirculation from the turbos.
Hope that helps.