Machine the flywheel. You don't want to have premature clutch failure. Why not get it machined during the week?
Get new bolts. Its not neccessary but if its all out why not. At the same time you can get pressure plate bolts too. Personally I don't really worry about them as they're not stretch bolts and if they look ok i tend to re use them (in my own cars that is).
You'll need a clutch alignment tool to get the friction plate aligned properly so you can put the gearbox in. Alternatively you can align it by eye, but if you have never done a clutch before i'd recommend getting the tool (its a special tool, you can get universal ones but they are usually crap).
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