Since you lowered the bike, you'll need to go to a larger front sprocket to keep the chain from wearing down the chain rubbing strip prematurely.
That will decrease torque and increase top speed (lower revs) from the stock set up. 2000 models already had different sprockets from the earlier models to decrease revs.
Since you want to ride two-up though, you may want more torque and higher revs to pull two people.
Therefore, you may want to think about buying a larger rear sprocket to accomplish that. It would also help raise the chain some more to accommodate the extra weight on the suspension.
The revs will be higher and it'll sound busy at 80 MPH but especially with a 900, you'll need the grunt of the larger rear to pull two people.