I have limited experience with 2 into 1 exhausts, but what experience I do have shows that 2 into 1s are not superior to the stock cross-over system.
The 'nostalgia' folks like to think that the 'good old days' had better engineering but that just ain't so. The 2 into 1 exhaust works best with a 360 degree parallel twin or a 'Boxer', both of which have even firing.
Like Reed has stated, the stock 900SS pipe diameter is the same as that of an 888. The 46mm (O.D.) pipe does cost a little HP above about 90HP but it does make a little more torque. That is the trade-off.
Below is a chart from last year ('99) of Reed's 1999 900SS. It shows the stock system with D&Ds and a Gio-Ca-Moto system with a Termignoni muffler grafted on. You will notice that the 2 into1 doesn't make more power or more torque.
The 2 into 1 does appear to tune at much higher RPM than the engine is capable. That should be a function of pipe length. (although, the diameter does influence the tuning RPM range by virtue of it's influence on the temp/density/speed-of-sound of the mixture.)
Below is a chart of a 900SS CR with a Stain-tune 2 into 1 and a 900SS with Micron slip-ons. Both have the air-box lid installed, but the 900 with the stock exhaust header has the 'snorkels' removed from the top.
You will notice that the 2 into 1 has more torque below 5500 RPM, and looks like it can make more above 8500.
Below 5500 RPM less than 57HP is available. So, it doesn't make the bike faster unless the operator doesn't know how to ride. And don't give me that crap about using the power at that RPM. Below 5000 you shouldn't be at WOT anyway and at part throttle the rider making throttle adjustments will make any difference in peak power potential, transparent.
Below I've compared a 984 engine with the stocker with the 2 into 1.
If you have a 'big' engine the power available below 5500 is even greater but 70HP still isn't the reason you put in all that hard work. Therefore, I feel that the 'more torque' argument is just an excuse for not doing your homework.
And, not just in this case, that's the classic argument of the H-D guys.