I can appreciate the creepiness. I had a lot of problems with my ESB-4 too, BTW, and got a lot of help from folks here. That’s what everyone here is for ;-)
It sounds like the problem is in the pocket since you seem to have done the glue up right! Vinegar was a good idea. I would recommend doing as little sanding as possible right now. Any material you take off might make the neck fit more loosely. That can be fixed with some veneer, but the less of that you have to do the better.
So, now that you have the neck off, you now have two problems. One is string rise. Strings need to be lower where they meet the bridge. The other problem is string alignment. The E and G strings need to be about equally distant from the sides of the neck.
First string rise…
When I look at this pic:
http://www.buildyourownguitar.com.au...6&d=1524061613
It looks about the way it should. The bridge end of the neck does not look too high at all. You can safely bring it down a bit, but not too much. What it really may need is to be raised a little bit at the headstock end of the pocket.
The simplest way to do this is with a shim. I know you can get these from Stew Mac:
http://www.stewmac.com/Materials_and..._for_Bass.html
http://www.stewmac.com/How-To/Tool_D...eck_Shims.html
Your shim will go in the opposite way from the one in the video. The thinnest part should be at the bridge end of the pocket. You may be able to get shims from other places, but the ones from SM are maple and that should be pretty good quality.
You can make a shim too, but it’s more work. You’ll need to experiment a little bit with a straight-edge to see where the angle is right. It does not take a very big angle to make a big difference. The 1 degree shim sold by Stew Mac should move the strings down by about ¼ inch. If that’s not enough, you can glue in another.
Test dry fitting a lot before gluing. ;-)
Ok, will send something on the alignment problem later...