Allow me guys.......
Welcome to the forum, and good choice of car!
I've got a couple of Supers, but have only briefly driven the Cloverleaf, as I bought one for parts, and only drove it round the block really. The Super is a far superior car, and I wouldn't even think of buying a Cloverleaf.
The most important differences are mechanical. The Super has lower gearing than the Cloverleaf, something not to be underestimated. The Cloverleaf was always criticised for having gearing far too high. I can believe this as even the Super has fairly high gearing. As an illustration, my standard Super is only just getting into fifth gear after the finish line at Phillip Island, at about 180km/h. It is fairly good for normal street driving however.
The Super also got stiffer suspension. Again this is still fairly soft for track work (search around this forum for a while and you'll see a few pics of mine on it's doorhandles), but is actually pretty good for road stuff. It's very comfortable, and although it rolls a bit, it does hold on really well. and can give you a moderately sporting drive if required.
The Super has the same suspension settings as the 75 V6 I believe, and it also got the better clutch from that car.
Other than that it's mainly cosmetic, although one important distinction is that the Super dropped the digital dash for the analogue one. I gather the digital dash is a pain in the a**e.
I haven't heard of any injection/rev changes, but I'm no expert.
There are certainly far less Supers around, as the Cloverleaf gave the car a bad name, so they struggled to sell. But they were a far better car, and rated by the Aussie media as a better all-round car than the 75 (2.5 V6).
There's a good website here
http://www.geocities.com/MotorCity/Downs/7709/alfa90.html with some information and manuals on the 90.
There's also a beautiful Super for sale on ebay at the moment. It's in NSW and it's not cheap, but I've seen the car and it looks almost like a new car. Probably one of the best around. No relation/friend of seller etc......
Good luck mate! Let us all know how your adventure goes.