I'm hoping some here can help me. I have completed my second 3 string guiter. The first one turned out great and sounds great in every way even though I have not learned to play yet.
My newest is also a three string built the same way with same pickup and all however....I can tune it to G,D,G and the tone is real good but when I push a string down the notes tend to sound sour. It never did this on my first guitar so I'm really confussed as tho what to look for.
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Without pictures, it will take a little guesswork, but here goes....
Sounds like you either have a higher action than your first build, or an intonation problem.
If the action is too high, meaning the strings are abnormally high off the fretboard, the pressure it takes to push the string down will change the tension enough to change, or "sour", the note. I would suggest looking at the first build to see if you notice a big difference.
Intonation is another possibility. If the bridge is not the correct distance from the nut, then the notes will be off at every fret. An easy way to check is to tune the guitar to G-D-G as you normally would with your tuner. Next, play each string at the 12th fret. If you are using a slide, take care that you are exactly on the fret. The same note, but one octave higher should show up on your tuner. If not you will have to adjust the bridge. Quick tip- Move a little and check alot. A little movement goes a long way.
Hope this helps.