If they are the stock cylinders just punched out to a 409 then you can still run the 2into1 carb and 2into1 pipe. But if you are going to restrict the larger size bores with the 2 into 1 setup you may has well keep your stock cylinders.
My .02 on woods racing,,, If you have your mind set on running a 2 stroke you have plenty of motor with what you have now. Spend all your resources on the very best suspension you can buy, some good skidplates and waterproofing. Then hope you have the nuts to hang on to that beotch thru the tight trails.