You are absolutely right that excessive nut height causes all sorts of evil influences - the slightest difference in cut height on the two B strings on a 12-string can result in a guitar that howls like a wolf when you play a root D chord or a G/D, just for example.

On my Mugen THE 78/12 Brian Rodgers (who I mentioned above) spent many happy hours getting it so the string heights were equal for each string in each course (ie the two bottom Es were the same height off the fret) and individually intoning each of the 12 strings at the saddle - and now I have one of the very few 12 strings that plays almost completely in tune almost all the way up the neck.

So any bad noises must be my fault!

Stick around and join in - we rant a lot about "what is folk" and politics, but the guitar threads are usually less hostile...