Congratulations on reaching the end of your journey! (Well, sort of - this journey never seems to really end. There's always something that will draw us back to fix or fiddle.)
re: low E intonation - There is definitely at least a few mm to be gained on that saddle. You can snip the spring in half (or as short as necessary). It looks like it's fully compressed at the moment and preventing any further movement back. I've even seen cases where the spring is removed completely. The spring does bugger-all once the string is on and under tension. This may not be considered optimal, but short of re-locating the bridge, it is a workable solution.
Now, I don't mean to rain or your parade, but I'd like to comment on the photos you posted of the nut. I'll apologise in advance if I'm being too critical. On the positive side, your break angle on the slots look really good!
However in the first photo, the top of the nut on the bass side appears to be sloping toward the fretboard rather than the headstock.
Typically when profiling the top of this style of nut, the high point should be on the fretboard side and slope away to the fretboard side. With sloping toward the headstock, the string slot depth is gradually diminished along its length. I know it's only travelling 3mm through the slot, but this is general accepted practise.
The treble side in the second photo looks to be sloping in the right direction but still quite high above the top of the string IMO. The overall string depth* is also deeper than I would have them, but fixing that and the profile is easily done with a flat file and sandpaper as well as being subject to opinion/personal preference.
*I recently commented about string slot depth twice in this thread in post
#153 and in my edit to post
#179.