You probably don't need to replace the valves, just clean the stems and lubricate the guides a bit. Also, for the cylinder that had the water in it, would be a good idea to check the valve/seat faces for slight surface rust (as you know water went through them). If either is pitted, it will probably be an issue as far as valve life. You'll need a big ole' flathead valve bar to pull the guides down - to remove the horseshoe guide retainer clip. As your engine was recently rebuilt, it should be an easy job.
If the valves/seats are just slightly rusted, you may want to clean the valves with a wire brush (on a bench grinder) then just lap them in with fine lapping compound - to ensure a good seal. Then lubricate the stem/guide before reassembly.
Best Procedure: If I had the engine down to this point, I'd probably do that on all cylinders. It isn't hard to do and helps guarantee a good combustion seal. As other noted - make sure you keep all the valves/guides together as sets and replace them back where they came from!
By pulling ALL the valves/guides you can clean them all up, clean the ports, lubricate the guides and reassemble them. My guess is that you could easily do ALL of this over a weekend.
Tip: I take a piece of 1/16" stiff wire (like a welding rod) and I make a "hook" on the end of it that fits in the horseshoe guide hole. Then I make a "finger pull loop" about 10" up on the wire and I use this to easily pull the clips out while I have the guide pulled down with the valve-bar in my other hand.