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First full setup - need help with intonation.

I picked up a used Squire Precision V for cheap, and have started working on the setup, using the FAQs here as a guide. Overall, it went pretty well. I replaced strings, adjusted the truss rod, and action. Fret buzz is way down, and play-ability is vastly improved.

The problem is with intonation. B and E's saddles don't have any more adjustment left in them, and are pretty sharp. Any thoughts? A, D and G are fine.

Thanks!
 
1. Witness points.
2. Nut.

Witness points are established by pushing down hard on the string in front of the saddle and the nut. The idea is to make sure that the string comes straight off and speaks from top dead center of the saddle and from the leading (bridge side) edge of the nut.

If the nut slots have a high spot behind (headstock side) the leading edge it effectively changes the scale length. Loosen the string, apply pencil lead to the bottom of the slot. Tighten and loosen the string a few times then look at the path. It should be worn to the leading edge. If it is not the nut is out of adjustment. The slot will have to be filed.
 
Saddles all the way to the tail? Good. If not, wind them back. Tune up, press down on on strings on both Sides of the saddles to make a good sharp bend and remove any string arc. Do the same at the nut. Tune up and check intonation. You'll probably be flat. Move saddles forward toward the pickups. Press the strings flat, tune up, check intonation. Repeat.

Once you get it in, next time you change strings you won't have to move very much if they are the same brand/gauge. Just remember to set "witness points" by bending the strings over the nut and saddles so the string has no arc.
 
Too late with my last post. Lol. What 202dy said.

The OP said his saddles are out of room and still sharp that would indicate he had moved them back to the tail all the way, at least until the springs were compressed totally. So it would seem, I could have read wrong.
 
Thanks, you've given me several things to try. One clarification - my saddles are fully extended away from the bridge, and they're still sharp. I'll move them back, try to establish the witness point, and let you know what the results are.
 
OK. This seems like an easy fix. It seemed like I was making it worse as I moved the saddles back, but maybe that was because I didn't re-tune?
Absolutely, and as you move the saddles back toward bridge/ball-end they are raising the strings. You move the saddles back 1/4", you'll probably have to turn the height screws 1-1.5 full turns to lower the string to prior height.
 
I took the saddles back as far as they could go without looking like they were stressing and pressed the strings down as instructed. After retuning, E was perfect. B needed a small nudge forward, but was fine after that move. Thanks, all of you! This was way easier than it seemed like it could have been.

Here is how it looks, post-adjustment:

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