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A way to get the height on the nut right is to press the strings down at the third fret, and see how much clearance there is over the first fret. You're looking for about 10 - 12 thousandths of an inch (or a tiny bit of clearance if you don't have feeler gauges). Ideally, you'll want to shave the bottom of the nut to get the height, unless you have nut files.
Once that's set, check the action the old fashion way. If it's high, shave the saddle down from the bottom edge.
It'll be worth noting that the neck relief may have changed if the strings have been off for a long time, so if you have a high action, make sure it's not too much relief in the neck. Depress a string at the 1st and 13th fret at the same time, and check the height above the 7th. Again, you're looking for about 10 thousandths. If it's higher than that, you need to tighten the truss; if the string hits the frets, you need to loosen it. Get a tech to do this if you're not confident with it, as I've seen stripped, snapped and broken truss rods from people going nuts with them.
Hope that helps.
Relief first - capo at first and fret at body join fret means nut and saddle are irrelevant.
Then nut - fret at 3rd fret and measure height of string at first
Then saddle for action.
Doesn't seem to bad now, a little room for adjustment on the saddle left.
Was told not to worry about slotting the saddle for the strings as they will make slight slots themselves.
Thanks everyone.
The B string intonation is fine but doesn't sound correct on the first fret, it is also difficult to fret, sounds fuzzy when playing a chord, fine when playing a single note.
Thanks of all the help.