to blame the finish on the paint seems a bit weird
I doubt that as the paint should be under layers of glass - The only issue with having too much paint is that the glass might not stick so great too it. But that will only happen if you have really overdone the painting. Usually this wouldnt be noticable but could suffer from quick delam later on.
Boards usually come in a SANDED finish. To get a glossy finish you usually have to pay extra in the states its usually $50 and is known as a gloss coat. I however think its completely pointless. However the sanded finish should not be rough. Well at least in my experience the boards i have had custom have been smooth to the touch. Even the boards i have made myself have been smooth so i dont know on that one
The stringer scratches are not that uncommon as each foam blank is slightly different. Good foam will be consisent quality between blanks. Bad foam can chip leaving small craters like a buck shot effect. Without pictures its impossible to know (although i doubt a photgraph will really show that up) In any case it could just be a few rough marks that were not sanded smooth
The bubbles - well a picture is really required. But for the most part you shouldnt really see any as buddles are caused by airpockets getting trapped in the fiber glass cloth while laminating another possible reason for air bubbles is that the board was shaped out of balance leaving indentations here and there which air can get under and cause a bubble these slight vairations in the board are hard to spot but should shine up under shaping lights pretty easily. If there are a lot of them and if the are big i would start to be highly suspect of the glass job.
The fin plugs - not that uncommon in some boards seen lots of boards with that (im assuming this is FCS) never happened to me personaly all my boards are future fin set-ups.
All in all its hard to judge without seeing any pictures or actually seeing the board for myself. But it sounds a little dodgy but like i say i couldnt really tell from here
However you should really quell your mind as if you are unsure about your board phycologically you will surf it crap. Im a big advocate of supporting local shapers but i do recognise the fact that not all of them are that great that is why always research your shaper beforehand. (im not saying the shaper who did your board is crap i dont know just shooting out a general warning to whoever reads this)