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mm,

I'm curious how you are sanding sides with a random orbit sander? Not sure how you would not over sand the high points and under sand the low points with the sides so curved. Not saying you can't, but I'm unsure how it would be done.

Do you think you have the sides nice and level (irregardless of sanding method)? When you sand down the zpoxy, you sand through first where the wood is highest leaving a lighter colored area. If you are doing this, you should start to see a little color in the dust from the wood (mine had a reddish color from the rosewood I was sanding). You see in the video that Todd works with hard block with cork on it to sand and level the sides and he uses PVC pipe with cork then sandpaper to sand the narrowest part of the waist. You might try that to get you sides nice and level. If the grain appears fuzzy in any spot, you likely have a low spot that isn't getting sanded. You can test by marking it with a pencil or chalk and resand to see if the chalk/pencil mark is being removed.

For the last coat, Todd puts on a very light coat of zpoxy, spreads it over the entire surface, then squeegees off every bit of it he can (holding the squegee in a very upright position to pull off as much as possible). This leaves a very thin coat......and per Todd, the purpose of this coat is to wet and color everything evenly so you don't have splotches. Todd doesn't sand this coat else you risk sanding through creating the splotches again.

mmpags,
Pictures would be helpful if you can post a couple. I will tell you what I am thinking anyway though. On my first build, I had some glue (Titebond) on my sapele sides that you could not see. Everything looked uniform in color before lacquer. When I started lacquering, the areas with the invisible glue were lighter than the rest of the wood because the lacquer was not penetrating in those areas. You may be having the same problem. If you wet the wood with alcohol or naphtha, does it all darken evenly? Thats a starting point.
Also, I saw a tutorial on another forum where after the guy was finished with all the coats of Z-Poxy and his sanding, he mixed a batch of Z-Poxy and thinned it with I believe alcohol, and then used a cotton cloth to apply a thin even coat to the whole surface. One of the problems with Z-Poxy is, if you sand it off in some spots and only have the pores filled, but other areas have it all over, you will get a splotchy finish when you lacquer. This is another thing you could try to get rid of the light areas.
Definitely post a pic or two if you can. It will really help us determine what is happening.

Tony

You don't have to take it all down, just apply one more very thin coat over everything. Then don't sand with a hard block and you should be able to keep a consistent color. Could be that the curve of the back is a little bit tighter at the waist?

It sounds like you are trying to leave a film of epoxy on the wood? I should think, and this is the way I do it, that it is better to fill the pores only. I scrape most of the epoxy off the surface with a razor blade, and then sand to the wood, leaving the epoxy in the pores. This usually takes 3 applications. I have seen where some actually coat the guitar with epoxy, but I would not think this is the best way. Put your finish over the wood, not over epoxy.

Kevin