#1
Whenever I tune up my guitar to standard pitch, the open strings sound alright, but the B and high E strings have bad intonation. The third fret of the B string (D) is way too sharp to be D. Whenever I play open D and 3rd fret B, the 3rd fret is too sharp. 5th fret on high E is also way too sharp to be A, but when it's open, it sounds fine.

The G string is the most serious problem though. Seventh fret is super sharp and I have to detune the G string slightly so that 7th fret D matches open D.

I'm not sure if hte problem is in the nut, the tuners, or the frets themselves.
#2
Welcome to the world of even tempered instruments!!!! The guitar's fretboard is a compromise and not entriely accurate.
To intonate your guitar, you need new strings with the guitar setup the way you like (string heigth, neck relief & Nut heigth). Then with a good guitar tuner you pluck an open string (Low E) and tune to pitch, careful not to keep you rhand on the tuning peg after you adjust pitch and check.
Now fret the twelve fret and check tuning again. If the fretted 12th note is sharp the string length is too short so you move your bridge saddle back (away from the nut) till they are the same. IF the 12th Fret note is too flat, the string is too long and you move the bridge saddle forward (towards the nut) until they match. Repeat for all strings and you're intonated!
Note some people prefer to use the harmonic at the twelveth fret instead of fretting the note but many luthiers say this doesn't compensate for string deflection which actually changes string length when you fret a note.
Moving on.....
#3
No, my axe is already perfectly intonated (just did it 4 days ago).

I've already known how to intonate it, but it's been like this ever since I bought it.
#5
you need to take it to a pro because if you set the intonation correctly and it is still not right you have a problem with something else.

KenG; I have always used the harmonic on the twelfth fret but what you say makes sense. I will set it using the fretted twelfth and see.
proud american
#6
Quote by jrnjd
you need to take it to a pro because if you set the intonation correctly and it is still not right you have a problem with something else.

KenG; I have always used the harmonic on the twelfth fret but what you say makes sense. I will set it using the fretted twelfth and see.



Yeah. I've heard of both methods and used the harmonic one myself for years. After buying Dan Erlewine's book and reading it I switched.
Moving on.....