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Additional update to add to list of mistakes:

I may have glued the bridge about 1/16" too forward. I was having intonation problems ever since I strung the guitar up and when I measured the distance from the nut to the contact point at the saddle I found that it was consistently about 1/16" too forward. How did I make such a mistake? I can't remember that clearly. Retracing my memory, the below are some candidates:

1. Measuring the scale length without a "nut" to stop the straight edge from moving.
2. Measuring the scale length from the nut to the edges of the saddle, NOT the 1 and 6 E string saddle locations.
3. Not marking the bridge positions with tape, etc, and not securing the bridge while I drilled the pilot holes.
4. Drilling the pilot holes first with a smaller bit then using a larger 3/16" bit. The 3/16" bit fills the hole and can't move around much, but a smaller bit can.

Also, my saddle leans backwards towards the bridge pins. When I lower the saddle height by sanding the bottom, the contact point moves forward. It seems like sanding the nut and saddle to get the setup the way I want will change the scale length bit by bit.

Thankfully I still have enough saddle that I could get better intonation by sanding the front of the saddle, so that the contact point is in the middle of the saddle.

The measured placement of the bridge is theoretical only. In practice, The saddle needs to end up maybe 1/8" back of where measurement would put it.

"Chimer" a string at the 12th fret, then fret the string at the 12th fret, and see how much difference in pitch you hear.

(Remember, the difference between theory and reality is that, in theory, there is no difference.)

MaineGeezer wrote: ↑Mon Jul 26, 2021 11:17 am The measured placement of the bridge is theoretical only. In practice, The saddle needs to end up maybe 1/8" back of where measurement would put it.

"Chimer" a string at the 12th fret, then fret the string at the 12th fret, and see how much difference in pitch you hear.

(Remember, the difference between theory and reality is that, in theory, there is no difference.)

Thanks for this tip! I checked the notes at the 12th fret and some strings are not too far off, but the low E string is way off! The fretted note is much higher than the harmonic. I'm guessing I should try to sand the saddle back to make the string longer? The A string and the B string and also have small differences, but it is not as pronounced as the Low E.

You did install the saddle at a slight angle to the strings, didn't you? (The treble end ought to be about 1/8" closer to the 12th fret than the bass end.)
Assuming you did, you'll just have to adjust where the strings contact the saddle. You can't do too much, but you can shift things a bit.

MaineGeezer wrote: ↑Tue Jul 27, 2021 8:29 pm You did install the saddle at a slight angle to the strings, didn't you? (The treble end ought to be about 1/8" closer to the 12th fret than the bass end.)
Assuming you did, you'll just have to adjust where the strings contact the saddle. You can't do too much, but you can shift things a bit.

Yes, Mr. Hall already set the saddle so that the treble side is closer than the bass end. I have been adjusting the top of the saddle, so it looks a bit like an arch. I'm trying to make the point of the arch go back a bit for each string (the low E and the B seem to need the most finessing). Is that similar to what you are talking about, adjusting where the string contacts the saddle? I just did a bit of finessing and the differences have gotten smaller, although it still exists for the low E and B.

Yes - The B tends to need tweaking, and the others may too. Here's a photo of a saddle set up by my luthier friend Carter Ruff:

MaineGeezer wrote: ↑Wed Jul 28, 2021 8:40 am Yes - The B tends to need tweaking, and the others may too. Here's a photo of a saddle set up by my luthier friend Carter Ruff:
DSC04787.JPG

Thanks! The B and the low E are way back! I don't think I have enough space to go as far back as the ones in your picture but hopefully it will get somewhat acceptable intonation.