Pretty bike... too bad about the engine. If you can turn a wrench, and are patient, then you should be able to rebuild that bike without an issue. If you are going to do it, then here's a decent set of steps to get you there.
1) Check the bores to see if they are within spec. If they are, then buy standard bore rings, have the cylinders honed, and you'll be ready to reassemble.
2) If the cylinders are not within spec, then decide how big you want to go and send them off to be bored.
a) Bob Hamilton (I can give you his number) in Virginia can do this for under $200.
b) a 466 kit off eBay is only $135 shipped, and I highly recommend it. Other overbores can be found on eBay too.
3) Buy a gasket kit for the upper and lower seals in the engine and replace them all (ask for more detail before you do this)
4) Check the timing chain components and replace whatever is worn.
It sounds like the first thing you should do it check the bore on the cylinders. The next thing is to check your timing chain components. Replacing the timing chain really isn't bad, and gives you an opportunity to replace all of the seals in the bottom of the engine and replace any roller bearings that might be worn out.
Once you decide your route, we can help you find parts and lay out a plan. I'm rebuilding another 400F engine right now, and can walk you through it pretty easily if you want.
Camelman