Introduction and NEED HELP

[Hazzerwaz]

Hi there. I'm new here. I own a 1999 XJ600N which I am customising into a cafe racer. Everything has been built up from scratch. Frame and tank repainted. New bearings in wheels new tyres, chain and sprockets.... My problem now is splitting the engine case to replace parts of the gearbox. I have all of the bolts out that the manual lists including the bolt under the oil filter and yet I cant get the cases to come apart. I still have the gear selector and rod installed but I haven't heard any mention of needing to remove that. If anyone can help me here it would be great.