Finishing can be very enjoyable if everything is working or amazingly frustrating if something isn't working! A heavy coat of EM6000 will really raise the grain. On a spruce top, the grain will look like mountains and valleys! Hardwood backs and sides usually don't react so much. But part of your waviness may simply be due to the grain raising from the moisture. If that is the case, aggressive leveling may be called for.
I usually don't level the first time until about the 6th coat, and I am pretty agressive. I use 400 grit and a Motorguard
rubber sanding block. I do just like Ken Cierp states and sand until all the glossy spots are gone except for a few pin holes from open pores. I rarely sand through to wood, but I am certain several coats get removed during this process. But once leveled, I can build up subsequent layers without worrying about a need for aggressive leveling again.
As far as how to level. I don't use a RO. All is done by hand and doesn't really take more than 30 to 60 minutes or so to do the body. I always sand from the center towards the edges, making sure to not apply too much pressure near the edge. In fact, I don't let sandpaper touch the edge line until I am all done spraying, and then I may only use 800 grit along that edge line. 400 grit paper along an edge will remove finish in a heartbeat. Make sure you have plenty of light, and situate yourself so you can see how the finish looks with every pass of the sanding block. Sneak up to the edges, and only remove enough finish to dull the entire surface. I use Klingspors good stearated paper for leveling, and to do the top, I'd likely use one to one and a half sheets of paper, cut into fourths. I'll work the sanding block from different angles to avoid sanding a groove in the surface and to keep the surface nice and level.
Once the big leveling is done, I'll shoot three to six more coats then start the drop filling to fill any open pores. To make spotting the pin holes easier, I lightly scuff the surface with 400 grit. After the pores have been drop filled, I'll level good with 400 grit then shoot more lacquer. Any subsequent sanding is done with 600 grit to avoid leaving scratch marks in the finish that could be visible beneath the finish later. Unless you have massive areas of open pores, I wouldn't sand back to bare wood. I'd simply get a fine modelers brush and put drops of fill in any remaining pores. If the pores are really deep, you may need to go over the pores twice.
I typically shoot three to six more coats to then finish up. Keep at it. If you remove too much finish, you can always build back up more coats. Then after a couple of guitars, you'll have it figured out!