when it comes to performance up grades whats the difference between the 2 systems?

I am trying to understand this also. What is the difference between MEFI 1, 2, 3, 4, 4A, and 4B? Can you upgrade - answer seems to be 'you must upgrade both ecm and harness'. Is that right? Can they all be reflashed? I assume the newer versions have more configuration options. Finally, what is the difference between the MSD, Delco, and Mercury 'MEFI' units?

http://74.125.93.132/search?q=cache:...&ct=clnk&gl=us

That should answer any question's

The Mefi 3 was mostly designed to use with a supercharger. The Mefi 1 and 2 do not have a provision for tuning in boost. The 3 has a boost compensation table to be able to tune the engine in boost. Not only that, the 3 just has a bunch more tunability. It's in boost tuning is crude compared to the 4.

The 1 and 2 are very similar. The 3 and 4 both have boost compensation tables. The 4 has much greater tunability when in boost. Yes, they can all be reflashed. You can re-pin any harness to work with the other. Some will require the addition of some wires, relays, etc. but the basic wiring can be used. Going from a 3 to a 4 is pretty easy. Any other, I just replace it rather than butchering a harness that isn't that great in the first place. The guy that builds my harnesses makes a first class harness that blows away the Merc. harness.
Everyone pretty much uses 4's now because of availability. The 3's are getting hard to come by and are getting expensive because of that. The 4 is pretty cheap at about $450. Some of the 3's from Merc. are over $1000. MSD and Painless both use a 4b. Merc. never used the 4 in a production engine. There isn't much difference in the 4a and 4B. However, the cals are not directly interchangable. You have to convert the files to use one in another.
In new engines, I strictly use a 4B. It is the latest and greatest of the Mefi's and has the greatest tunability. It is a very advanced ecm. I can tune and have used them all, but I prefer the 4B on a new build, especially supercharged.(but I do use them on NA engines as well) Hope this helps explain it some.
Eddie

Eddie - would like to talk to you about a 4b and harness. I'm currently using a MEFI 1 with a boost-ref fuel regulator. Will you be available for a quick phone call sometime next week?

Certainly. Call anytime. If you can't get me on the shop # (615-216-7449), then try my cell. (504-416-3607) Look forward to hearing from you.
Eddie