Swapping the new rock for the old rock is a matter of letting the biofilter establish itself enough on the new rock to handle the bio load after you take out the old rock. In your case, you only have four fish (the coral isn't as much of an issue). What kind of rock will you be adding, and do you think it will be about the same amount as the old rock?
The bacteria will populate everything that the water touches, so your sump, the frag tank, the new sand, etc is all surface area for the bacteria. You could probably do the swap pretty quickly (as in all of it at once), but the best way to tell if you are moving too fast is to watch your ammonia levels.
The risk you take having both new and old rock in the system for a long period of time is that the bubble algae will establish itself on the new rock. It's probably on your frag plugs, so unless you plan to clear all of that (remove frags from plugs, etc), you can be careful with the rock and not add to the risk that the frag plugs already represent.
I hate bubble algae. Most likely you will find that despite taking as much care as possible, it may show up anyway. Key thing is to jump on it right away. And with your stocking list, an emerald crab won't be a bad idea (the ones from reefcleaners.org always seem to work for me).
