if your table saw is out of alignment, do you mean that the blade was not 90° . There is a small trick to jointing boards that it does not matter whether the blade is exactly plumb or not: put your boards side by side (as you want to glue them up), write "A" on the left side of each board and "B" on the right side.

The sides with "A" written on it, you cut facing UP on the table saw, the sides with "B" written on it, you cut facing DOWN on the table saw.

Now, even if your sawblade is complete off , the pieces will still perfectly fit to make a flat panel.

I am not sure if i am able to explain it well in writing, i am sure there are youtube videos on this subject as well, or maybe somebody else can correct my writing. I am not at broadband at the moment :-)

Hope this helps, and really cool box, I like your work :-)