I also am not an expert here but I have built a few Gibson style instruments and experimented with finishing. First, I would try to sand out the dings - any filler will show under your 'burst and clear coats. Second, as you know, there are at least two ways to do 'bursts - you can stain the wood and apply clear over it, seal the wood and shoot the 'burst as the first few coats and then clear, or do both. They have different results - applying the stain directly to the wood will pop the grain and usually look deeper but it can be hard to control. Applying the color in the lacquer itself is much easier and if you screw up it is pretty easy to sand back. I have had acceptable results applying a stain designed to pop the figure, sealing that and then doing my burst in the lacquer, followed by clear. Gibson has used different variations on this thru the years - maybe Brian would comment.
You will also have the decision about whether to mask or scrape binding, this goes along with your head logo question. If you apply too many color coats before you scrape or pull the tape you will get a ledge - subsequent clear will at least partially reduce that. Again I have had acceptable results just scraping back and shooting the clear.
I was asked to add a pearl headstock inlay to a guitar with a black headplate. I sanded all the old finish off, inlayed the pearl, shot a couple of coats of vinyl sealer, then black, scraped back and then 6 or 8 or so coats of clear. Color sanding and buffed as usual - you can't see the edges.