IMO you should leave the pistons/rings/conrods alone, considering the reason you are stripping the bike.
You probably don't even need to remove the head to do transmission work.
Have seen the insides of several R3 engines with mileage similar to yours, and the bores and pistons were as new. The alloy liners are nickasil coated and the original factory criss-cross honing marks will look virtually untouched. I reckon in normal use they would last several hundred thousand miles.
IF you were to split the big-end or main bearings, it wouldn't do any harm to rebuild with new shells, they are pretty cheap. But even if you do, you'll see that the shells look almost unworn. Just make sure you get the right size shells if you decide to replace them. On the edge of the shells is a colour mark which designates their size... red, blue, white... probably rebuild with the same size....
Others will be along shortly with comments.....