I would do the stoker. Have they cylinders ported for what ever type of riding and for the 4mill stroker crank. That way you dont have to run one of those spacer plates inbetween the cylinders and cases.
What bore are your cylinders on now? I dont think I would bore a set of 64mm cylinders out to 66mm just to make a 400cc machine.
I found a set of patriot racing 4mill drag ported cylinder on here for around a $100 bucks. They needed resleeved. So I sent them back to Dan at Patriot Racing and had him resleeve them with cylinders that started out at 66mm and go all the way up to 68mm on there last bore. If your cylinders are at 65mm now you could have them bored out to 66mm, and next time it needs bored have them resleeved to start out at 66mm like I did. I got about $600 in my cylinders including the 100 bucks they cost me to buy them. Yea a couple hundred more and I could have just gotten a cub. The Stealth Look is kind of worth it though.