You are right about rejetting. It means that you either buy and put in larger or smaller jets to compensate for any changes made to the air filtering, or engine modifications, or changes in the exhaust, that will have an effect on the flow through the engine. And with the changes you have done, you will most likely need bigger jets.
The jet sizes used by others, with the same mods made to their bikes, might give you a hint, but there are only one way to find out what jet sizes that will work on your bike, and that is by testing them out. I would also wait with the jetting till you have put on the K&N filters, since they will most likeley require more rejetting if you don't wait.
I hope you will find this jetting guide helpful. If you scroll all the way down you will also see that it have an advice about jetting and altitude:
www.motorcyclecarbs.com/Jetting_Rules_of_Thumb_W43C551.cfm
But it will be a trial and error issue. And don't make more than one change at a time. Otherwise you will loose track of what you are doing. And personally I have found that CV carbs are running just as well, even better, on my 400 twin, with the stock air filter box.
Anyway, good luck.