If it’s an FZS600 (your profile says FZ6) then access is OK for changing the selector drum and forks with the engine in-situ.
However, the usual 2nd gear problem only affects that gear… the bike would run normally in neutral, first and, if you can persuade the selector past 2nd, the higher gears too. If yours is making a nasty racket as soon as the clutch is released then there is something else wrong. Hopefully it’s the clutch as that should be fixable, otherwise a replacement engine is the easier solution... replacing broken cogs in the box is a lot of work.