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Gotoh 3 saddle bridge from Warmoth Issues

For nut slot, capo fret one. You want the strings to just high enough that they ring out (IE high enough to clear fret 2). As a rule of thumb, the Ws nuts are often not slotted deep enough. But that is largely no harm no foul.

Order to address:

1. LOWER all the pups so they are barely above the pickguard. Then report back. I say this as what you are describing could easily be Stratitis. What you are experiencing is the exact symptoms of it.

It show up as you go higher on the neck as by fretting that high, you are further decreasing the distance from the pup to the strings.
Not sure if I installed the neck pickup wrong, but I can only get it to about an 1/8 above the pickguard before the screws go loose and the pickup moves around or put another way doesn't securely attach to the guitar. Do I need to remove the pickguard and check the install?

One more dumb question: When I fret a string going up the fretboard should they be in tune at every fret? I assume so. For example, on the low E string, if I fret the 5th fret, the A note, it should be in tune exactly at A? None of my notes are on any string. For the A on the 5th fret, it is sharp.
 
Intonation is a compromise. Sharp is how it will go with stratitis.
We want that neck pickup also decked to the Pickguard. As a starting point I run my neck pup 1/32 off the deck on the E side, 2/32 on the e side.

By chance are using using stacked coil pups?
 
Intonation is a compromise. Sharp is how it will go with stratitis.
We want that neck pickup also decked to the Pickguard. As a starting point I run my neck pup 1/32 off the deck on the E side, 2/32 on the e side.

By chance are using using stacked coil pups?
Just standard Fralin Blues Special pickups, the neck is open top though if that matters.
 
Is your neck pup wood mounted or Pickguard suspended?
Pickguard mounted.
Just standard Fralin Blues Special pickups, the neck is open top though if that matters.

is it wood mounted or body mounted? 1/8 is sitting pretty high.
It is pickguard mounted. I don't know why I can't lower them more without the screws seeming to get loose. Hopefully I can remove the pickguard without removing the strings and check the installation of the neck pickup. I don't recall any issues but for some reason when I lower the neck pickup to below 1/8" the screws seem like they are loose and not making contact and the pickup moves around, not sitting securely on the pickguard.
 
Stretch out the spring or get longer tubing. You're losing tension.
Then I need to remove the pickguard. i was hoping to avoid that. Perhaps I should contact Fralin and ask them for new springs and tubing?
I have to say I am less satisfied with this purchase from Fralin. My bridge pickup, when looking down while playing, has a place where there is a gap in the string and wire is showing. Fralin says they check 3 times (and my thoughts are why 3, why not 2, why not just say thoroughly checked?) so I had to have done it. I doubt that as I was very careful as always installing it as tele bridge pickups require a bit more care due to the thin wires.
 
Update: Fralin is sending me some tubing in the mail. Shouldn't be a problem to make sure I can adjust the neck pickup height now. I ordered the other tools needed and they should arrive by this weekend. My remaining issue is I can't seem to find a philips screwdriver that securely fits in the intonation screw for the bridge I have, the Gotoh Vintage Tele bridge with In Tune saddles. I was told it was a #2 PH but that is clearly too big. I have a Makita Impact Driver and I checked the bits I have for that. It seems to be a #1 PH, but there are different shapes of #1 PH in my bit set. There is one that fits cleanly but I can't find a manual screwdriver with the #1 head that is that specific shape like the one in my Makita Impact

I did see on a site selling the saddles the following spec:
  • Intonation adjustment screws - Metric M3-0.5 x 30mm

Driver bit set.
Does anyone have a link (other than Amazon) for a screwdriver that securely fits the Gotoh bridge intonation screws?

Edit: Looks like 3mm PH is a #1 PH. I do though wish someone could recommend a specific PH screwdriver that they know works with the Gotoh intonation screws.
 
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I just checked, PH2 (Phillips #2) fits in mine and I have the same bridge.

It's important to tune down the strings that are affected by the saddle you want to move. With the strings at full tension, you might damage the screw heads or the threads.

It's always:
-> Check the intonation;
-> if the fretted note is too high, tune down the string(s) and move the saddle away from the neck;
-> if the fretted note is too low, tune down the string(s) and move the saddle towards the neck;
-> if the fretted note is correct, go on with the next string
-> after moving the saddle, tune the string(s) back up to pitch and start again
 
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I just checked, PH2 (Phillips #2) fits in mine and I have the same bridge.

It's important to tune down the strings that are affected by the saddle you want to move. With the strings at full tension, you might damage the screw heads or the threads.

It's always:
-> Check the intonation;
-> if the fretted note is too high, tune down the string(s) and move the saddle away from the neck;
-> if the fretted note is too low, tune down the string(s) and move the saddle towards the neck;
-> if the fretted note is correct, go on with the next string
-> after moving the saddle, tune the string(s) back up to pitch and start again
Strange that you, and Spike from Warmoth both have experience using a #2 PH. I tried more than one and they seem too large and don't securely sit in the screw head. And again, in my Makita bit set there is a #1 PH that fits perfectly, the issue is it is for an impact driver and two things I am fairly certain of are (1) the adjustments shouldn't be done with a power tool, and (2) I shouldn't use a magnetic bit.

When my maintenance tools come this weekend I am going to do all of the measurements you and Tburst indicated. For now I can get the guitar playable and in pitfch on the open notes. When I move up the fretboard if I press lightly the notes are close to pitch, but a bit sharp. If I press harder as I would when playing, they are more sharp. On my Fractal Fm3 tuner they are still visual on the tuner display, but sharp by about 2 inches to the right of center (if that makes any sense).
 
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