After doing my JDM swap an injector went bad (Yea, that was fun troubleshooting).  I tried swapping an injector from the JDM (a 95 or lower block) but it failed to function as well.  I noticed the design was a bit different, is there a difference between the 96 model year and older injectors for the Multi-Port injection based 16 valve engines?

I would expect so, earlier models are batch fired not sequential so I would expect an earlier injector to have half the flow rate of a later injector. Are there any markings on the injectors?

No, just a different jet style setup and one is pink and the other has a white label.

The 96 has 4 small jets where the other motor had two large ones.  I don't have a manual for a pre-96 16 valve or I would check the specifications to see if there is a change.

Fun fact, the 96 is batch fire on start-up.  It will fire every time the crank position sensor goes off.  Once the engine starts it switches over to a batch mode.  Then to sequential once the engine starts to warm up. 

Fun fact, the 96 is batch fire on start-up.  It will fire every time the crank position sensor goes off.  Once the engine starts it switches over to a batch mode.  Then to sequential once the engine starts to warm up. 

Some of them also switch back to batch firing when you floor the throttle in order to get enough fuel enrichment.