Don't know all the details, but the '94 would have a lower plenum (more hood clearance) most likely and the shorter front accessory drive system and water pump.
The computer and harness are slightly different, so possibly the location of the sensors is suspect with regard to your current harness.
Otherwise, I'd bet that all the earlier stuff would still bolt right up to your engine. Firing order should be the same HO setup of most later 5.0's (13726548).
I have a standard '94 intake, and it's different than the others, but not radically. Not sure just what made a Cobra a Cobra in that year. Ryan does offer a '94/'95 harness too though, if you decide to go with all the '94 stuff.
Here again though, you might run afoul of different connectors on things like the MAF sensor and TPS and things like that, where Ford used several different types over the years.
Obviously, I'm just yappin', since I don't KNOW any of this from experience. I've seen the Cobra stuff mentioned fairly often here though, so someone should know what you need to make it work.
Good luck.
Paul