need help with intonation

I was doubling a guitar line last night(in E) and realized when I slid up to 
the 5 draw I was bending it just a tiny bit, but enough so it jarred with the 
guitar note. Then I realized that what I thought was poor tone, a little 
treble and thin, was actually out of tune notes. This is discouraging 
considering I've been playing for 30 years and just noticed this. How do I 
practice to correct this. It's usually the 5 and 6 draw. The harp's not out of 
tune. I can hit the note when I just single out that one hole.

Thanks in advance.

Rainbow Jimmy

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