I'd go for the newer bike, just for parts and the pita factor.
Look on ebay and see how many parts are for sale for each bike.
While researching carb/fuel injected for my hybrid project, it turns out that Honda only introduced fuel injection in their CBR series in 2000 or 2001, and hence the FI after the model name. So I'd be surprised if the '96 was fuel injected. I'd try to buy a carb for it online, if you find one then it's not fuel injected.
Or just ask the owner.
You can mess with carbs, but for fuel economy it's probably easier to find an aftermarket ecu that you can reprogram to fit your needs. That was the deciding factor for my decision to go with FI, but I don't know if there is an aftermarket ECU for your '96 bike.
Tom.