dude, what are you talking about stripping the nikasil? is something wrong with it? ONE of the main reasons its there is b/c it will make the cylinder last longer (ie, old cast cylinders used to wear AND the piston would wear) - now with the plating, the wear will be on the piston - and IN MOST cases, not the cylinder....so that when you rebuild, you are simply replacing the piston and not worrying about the cylinder being out of round, worn past specs, FORCING you to bore, etc...NOW if you really want to do a larger bore take the cylinder to a machine shop - they will bore out what you have and then either replate or sleeve the cylinder
pull the top end and inspect it...plating still there and in good shape? if so, clean the p-valve and order a STOCK sized piston.....of course measure the bore and make sure its good.
while you are there, check the crank - measure for side deflection and MOST importantly, up and down play....if its TIGHT, try rocking it by grabbing the flywheel - if there is not rocking, the bearings are fine. If they check out, ride the bike....bikes are like anything mechanical - if they are in spec, they are in spec....if not, fix what's wrong. hope that helps...
what the shop told you was correct - you don't bore a plated cylinder as part of routine rebuilds..if you want to step up the motor size - different story.