Our ear is very off when measuring pitch. Remember guitar mags with ads for tape lessons to learn the perfect pitch, haha..... these ads has being running since the 80's. Just like photographic memory, it's like natural talent, most don't have it, a few have it, and the few who have it and plays music are even less few.
Best to get a tuner like boss or korg ones, good and lasting. Learn to use it to tune down 1/2 or most 1 step. the guitar don't like to go beyond that normally. Your string tensions gets messed up and you get lousy tone.
When your guitar without strings, the nut and bridge/saddle groove, use the pencil to "marker" it. Don't be shy, rub as much in as you can. You can do so every time you change strings.
Hope it helps.
Heh will be getting a tuner when i have the $$...right now saving up for pickups. Anyway the groove is the thing at the headstock where the strings passed through right?
Regards
Mike
Mikemann Music Studio