Thanks for the detailed response, at first it seemed like a very labor intensive fix. I wish I could just sweep and loft planes.
I hope it will not come through as a waste of your time, but I tried one more thing before your solution .
It's not elegant, it's really dumb, but so far it seems to be working.
All I did was to overlap the single surfaces by a fraction of a millimeter, turn them to shells, so the shells overlap, I still can't union them nicely or at all, but the slicer software I use for 3d printing does union them during slicing.
I attached a photo, it's a before and after.
I still have one tiny gap on the newest iteration.
I hope this is going to work now, thanks for the help.