Toddler68, those little things mentioned to me are what give a completely handmade instrument individuality and character. Don't sweat it, man... My guitars will all have little "Character Flaws" in them too as we are not making CNC cookie-cutter instruments. You are doing awesome work, and your co-worker will be THRILLED with it, I'm sure. I know I would be...
I am surprised that the top is so thick... I typically use 1/4 inch thick tops and backs or less for my chambered body guitars. Are you concerned that it may be a bit bright in tone with all that maple and being a neck-through? It should sustain to infinity and beyond though!! Boggs