Personally I doubt that there will be much between them in weight, if anything the 900SSie engine would probably be lighter given the modern updates it got over the 900 carb engine that was the basis for the 750.
If you compare weights of the whole bikes, the 1991 750SS was listed at 173kg dry weight compared to 188kg dry for the 2000 900SSie.
If you want to go really mad, get an 1100 engine from an early Hypermotard as they're 177kg dry weight but have 90hp and you can free a few more ponies and kg with the single can exhaust, probably double what a 750SS will put out
The IE models are also far less complicated to setup than a carby engine (again, IMHO!) with little difference again between a set of throttle bodies and a set of carbs.
In terms of strength... improvements in technology between a 1991 and a 2008 engine should be a no-brainer.