I purchased a R&D head with flat top domes for what at the time seemed like a deal. I didn't know at the time that the flat top pistons that I bought ( another "deal") had a 4mm shorter compression height, now I'm trying to build a engine with what I have.
What CC? probably 23cc or 26cc. If you take material off the bottom and cut the sleeves back so they will fit in the cases you are still going to need domes in the 30's not 20's. Nobody ever made flat top domes bigger than about 26cc for the Yamaha in the flat top configuration because nobody did what you thinking of doing.
What was normally done, remove sleeves, machine off deck, bore for bigger sleeve, and pocket for sleeve head. Then port to new sleeve. The flat top sleeves have much much bigger ports that the cylinder needs to be ported to. Lots of people preport with a slave sleeve to mark. THe advantage is you go from super low port timing to race timing without have to weld.
Advice - Get rid of you flat domes and flat pistons. Do you know if your pistons are Kawasaki or R&D Dominator Yamaha's (Kawasaki forgings modified) what size are they? In mid 90's they made 80-81 then in the superstock era 84-86.5mm (This stuff is still on R&D's website) Are they big pin or Yamaha pin? I've owned BOTH...
IF you dont understand everything I would recommend SELLING......