No, you don't lap the bore with the piston or the piston with the bore, depending on how you want to look at it. If you try doing it that way, you have no control over what gets taken off where. You need an internal lap for the bore, and an external lap for the piston, if you want to lap both of them.
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I'm not sure if you are referring to the above link to the Super Tigres but I would like to point out that this does not show lapping the bore with the piston or the other way round - both liner and piston are individually lapped before lapping the piston to the bore. This method has ben used on several diesel engine builds with total success giving perfect fit and superb compression. I make no claim to the method - that must go to George Aldrich a well know engine rebuilder and tuner sadly no longer with us. A specialist in fitting piston and liners this was the method described by him in Strictly I/C and in Model Airplane News where he ran a regular column. George earnt his living in later life reworking piston and liners on small I/C engines for competitive and sport aeromodellers world wide.
Ramon