Howdy. This is probably a classic 'set up' conundrum of saddles vs. relief. The norm is for there to be some minimum neck relief set first then adjust final string height using the saddles. However, if you're ignoring the relief side of the equation and working towards a flatter neck then saddle heights are all you have an you're lowest action is determined by the precision of everything else, construction neck set and angle, fret work, etc. There is a limit to everything relative to playing style and string excursion. But lets keep it simple. Fist thing is that you need a small, inexpensive machinist ruler with whatever graduations you're comfortable and you need to take actual unfretted measurements at the 12th fret. That will insure that you have even relative string heights set with the saddles. You can also get your current string heights. You need this baseline data. After that you will know with certainty if the high E is simply lower than the rest even if only by 1/64". Hard to eyeball but at the limits enough to be your problem. After that what are the actual string heights vs. what you prefer vs. what EBMM specs are? My Axis SS sits at 3.5/64" to 4/64" for the low E to 3/64" on the high E gradually lowering as we measure across the 12th fret. I also have minimal neck relief, but I do have some. I think the EBMM guitars are exceptional in their fretwork from the start so a high fret, while not impossible, is unlikely. But that's an easy check with a fret rocker. Another cheap but vital tool for the set up arsenal. The flatter the neck setting the more saddle height you need to compensate.
From the EBMM set up instructions:
"First, check relief in the neck by holding the lowest (bass) string down on the second fret with your fretting hand, then hold it down on the 12th fret with your right thumb and tap on the string in the middle to show how straight the string is. It should be no more than the thickness of a thick business card. If there is no relief in the neck, applying a little pressure in the middle of the neck (downward) after adjusting the truss rod wheel should take care of it. If not, please contact us as it may be necessary to send the instrument to the factory.
Factory string setting for standard tuning starts at the bass side 2/32" (1.59 mm) to 5/64" (1.98 mm) and the treble side is 3/64" (1.19 mm) to 2/32" (1.59 mm) measured from the 12th fret to the bottom of the strings. The top of the strings should have the radius of the fretboard when you are looking at the strings in the playing position and by rotating the instrument while at the same time bringing strings into view one at a time. Remember, string height is ultimately determined by your preference and playing style.
Now, you are ready to play your guitar. If a string buzzes on an open string to the 5th fret and no higher, more relief is needed. If there is more buzz from the 5th to the 12th fret, the neck needs to be straighter. You should check the string height after every adjustment. If the buzzing happens throughout the neck, the string height needs to be increased.
Experiment a little to get the exact action you want."
