I've done a bit of refinishing on garage sale furniture (solid cherry night stands, solid maple coffee table and end tables, solid birch bedroom set, etc...) and I've found the best results are to be had by applying the clear coat with a small cloth (not a brush), allowing it to dry completely, then using something like steel wool to buff off any bubbles, and covering it again with clear coat. It won't ever be perfect so once you get it done to where you're satisfied - STOP!
As far as that one spot goes, why not just slap some stain on the exposed part, let dry and re-cover with the clear?
