Based on some of the home made foils that I have been able to ride I do not think that the few imperfections will make it impossible to ride. BUT, what I find much more important than the alignments and finishing is the strength and stiffness. The foil must be very solid. I find it possible to ride a foil that is even worse misaligned but solid to be much easier than a perfectly aligned foil that flex when you ride. I would suggest spending time making everything stiff (even if you thicken it up with lots of glass) and making the joints really solid.
Then once you have tested it, you could spend timeon making hte finishing beautiful.
Remember to leave a way of changing the rear wing angle. It is quite important to tune the rear wing angle to get a foil to be nice and stable and with low drag. A badly tuned rear wing can add more drag than a lot of surface imperfaction and distortions.
In very flat water and light wind you can get away with a sligtly less solid foil, but at best you will get sudden stalls where the foil throws you off, and at worst the foil could break while you ride (which has happended to me twice!)
Exactly, I found bamboo wood have resonance that will create huge vibration if too high aspect ratio even reinforcement with glass doesn't help. The low aspect ratio wings seem to work better. For high AR wing like yours, maybe a hardwood, carbon, aluminum or Titanium will work better.