I wouldn't pay a premium for a 96. In fact I'd pay substantially less. 96 made a lot of unfortunate changes on its way out. There were few put on the road. 95-96 specific parts are typically harder to find and a lot of the OEM parts are no longer available. 96 is missing VTC which is a big hit to power. The OBDII is harder to deal with and to my knowledge most of the tuners won't deal with them.
Don't think just because its a 96 that newer is better. Even at 18 years old, it really depends a lot on the mileage, how its been stored and how its been treated. A 90 that's been garaged and treated gently it's whole life is going to be in better shape than a 96 that's always lived outside and ragged on. In either case, whether the rubber parts on the car is 18 or 24 years old, they are probably dead or on their way out. There's going to be a maintenance, and its still going to be a fickle car.
IMO the best year to get is a 94. It had all of the refresh updates before they started really changing a bunch of things.
Anyways, to answer your question, the biggest tell-tale sign of whether its a 96 or not is if it has VTC solenoids. Checking the ECU to see if its the OBDII will tell you if its 95-96 or other. Other than that, there aren't a lot of specific things to look for on just the engine.
Other difference on a JDM engine is that the oil pressure sender will be located on the "left" side of the car instead of the right side. Also, it will likely have an old style PTU still because they didn't issue the recall there.
Not sure where they stamp the VIN on the engine.
http://z32.wikispaces.com/Year+Differences
http://z32.wikispaces.com/Production