I am fitting new cork seals on the side covers. How tight should the bolt be done up?

If they are the raise type, 2 ft/lbs and the depressed type 5 ft/lbs. See if you can get a hold of the Neoprene ones, they are much better.

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How can I tell the difference between raised and depressed?

With the raise ones the centre where the bolt goes through, sits higher than the gasket face. The depressed one is the other way.

Any chance of a pic?

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