The bottom part of the fret board or high E raises up way higher than the low E end. To the point that when I test the strings the high E is touching the frets. The neck feels unbalanced in the pocket making it hard to glue.
I am not sure I understand exactly what's going on with the neck from either thread, but a couple of things occur to me. The first thing to do is determine whether the neck is usable.
If the neck is twisted, that's a fatal flaw and will require replacing the neck. This could result in the problem you mentioned, particularly if the high strings touch the frets just on one part of the neck (eg. close to heel or close to the nut.
If it the neck is higher on one side than other, it may not be fatal. I have a bass neck where the fretboard is about 1.5mm higher on the treble side than the bass side. It's not twisted, the It's higher at the nut and at the heel. It was easy enough to compensate for this by doing two things: Raising the bridge a bit higher on the treble side than the bass side, and replacing the nut so that the slots could be cut to compensate.
I don't know which problem your neck has, but maybe one of them?
Not sure what you mean by the neck feeling "unbalanced." I have only done one set-neck guitar. The neck should feel tight in the pocket. If it does not feel tight when seated properly (e.g. moves laterally) or it has gaps at the heel end, or the angle is too low or two high for the bridge...these things would be problems that need to be addressed...but would require pics or more description or both to properly diagnose.
FFS, Fender, I’m trying to keep everything in one place (as we don’t seem to have any mods any more) and you go and mess things up. This isn’t the forum for this sort of question.