From what I see, I think you have set your self up for two things. One simple, one not so.
First as already mentioned, take the bare head to a machine shop and have it surfaced. Talk to the local M/C shops and see who they use. Any shop and do it, but a shop that doese a lot of bike work will have a lot less set up time an time is money.
The second part is that now you will need a valve job. If I were doing it, I would have a 3 angle valve job done. The problem is that you should do the whole thing. That means guides and seals. On jap bikes, guides are oversize and have to be reamed to the correct size. Not that hard, but you have to have the tools. In addition, most will say on this bike you don't grind the valves, You have new seats cut, and most will replace the valves. Again, this is all stuff you can do yourself, but the tools can get real costly. If I were in your spot I would contact someone like Honda Man and show him what you have, explain where you want to be, and see if he will do the work for you. THis part is NOT going to be cheap. And it will take some time to get one.
I would not worry about the chambers (other then the valves). Your not going to be racing the bike, I very much doubt it will be any sort of problem for you.