I had almost the same issues on my LP build. Check my signature. I als had a misaligned join in the bookmatched veneer but when I did a mock up I noticed that the neck and bridge positions were ok. So I decided to let the skewed veneer join to be as it is. Al long as the neck and bridge position is ok I'm ok.
I also had the neck that felt a bit wobbly when I did dry fit but I managed to correct this by chiseling of a very thin slice from the heel of the neck and just kept checking by dry fitting.
Overall I feel as if your kit was manufactured by the same person as mine...
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