What to do about upgrading "main" cluster from 8.4 to 9.1 when a 9.1 "main" already exists?
If the existing main is the default cluster that was created with your installation you can just drop it. Use the tool provided by your installation:
pg_dropcluster --stop 9.1 main

More info: man pg_dropcluster
There is nothing special about the main cluster. It's just a cluster like any other which happens to be the default in your installation.
If you haven't worked with the cluster yet, there is nothing in there, that you would lose. But check with psql or pgAdmin (or a client of your choosing) to make sure.