Yes, when you're getting good solder flow & wetting, there should be some (not a lot!) solder coming through the eyelets to the component side of the board.
None of the wiring mistakes you describe would do any damage.
A common mistake on this build is miswiring the input jack. It happens because the input uses a mono jack unlike most of the BYOC effects. So the sleeve and tip tabs end up on the opposite sides of the jack vs. a stereo jack. I rotate the jack around so that the long tip "finger" is on top, which keeps the wire runs to the PCB short. See "gut shot" of my Divided Octave below.
If that's not your problem, we need to see photos....
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