Might be just a little thing, but I think you need a space after the -P and before the port number. Or is that just a transcription error?
To prevent connecting to the otherinstances, you could stop all of them except the one you want to work on.
If the instance won't even start, then I don't think most of the tools will work either. It must have something fairly major wrong to cause it not to even start. Presumably you have an older version of MySQL that it will work with (that you're upgrading from) - can you run an older instance that doesn't need the upgrade and repair all your tables before retrying the upgrade? Or even do a dump and load from the old version into the new (should be fine as far as replication goes) instead of doing an in-place upgrade.
You could also try running mysqlcheck manually rather than via mysql_upgrade.