Hey I'm very new to electric guitars, so please have patience with me.
I've build a guitar from the cheapest strat kit on ebay and with new pickups and bridge it actually feels pretty good.
But sadly I have big intonation problems and there are so many possible reasons.
I set up the intonation so that the 12 fret is in tune. But now all the notes on the lower frets are sharp and even on the higher frets I get sharp notes when I press a little bit to hard (bar chords especially).
The solutions I thought of are:
- sanding deeper groves at the nut (I'm scared of overdoing it and the strings buzzing)
- shimming the neck (maybe the neck is just a bit to tilted)
- truss rod adjustment (but my truss rod feels like it's already on its limit. Maybe I just got a bad one (the kit was only 50 bucks))
- sanding the frets (should the string touch the fret board when fretted or not?? Maybe they are just to high)
- Any other things I might have forgotten???

I would send you pictures, but I don't know of what exactly. Let me know where and I will take pictures

Thanks for helping me find and fix my problems