rhoads56: Let's take your criticisms point by point, shall we?
Like I said, adjusting the truss rod doesn't change the scale much, but it does. It's a very slight change, but it's there. You can see this for yourself. Set up a guitar to have no relief, set your string height, then set the intonation. Now add some relief, set the string height to the same, and check your intonation again. It'll be close, but definitely off. It's a very slight change, but it's there and it's important to know this.
You're partially right on the point about the truss rod being related to string height. I should have been more specific. I will now point out that this advice is for JACKSONS and not Fenders or similar vintage-style guitars. Jacksons need straight necks, no relief, and so the truss rod should not factor into string height at all.
And you're being a jerk for no particular reason. No, this isn't related to intonation but it IS related to why a Jackson needs no relief. Excuse the hell out of me for feeling compelled to explain why something works a certain way instead of just saying "Make the board flat" and moving on.
When did I ever say it wasn't? I do believe I said "A properly setup guitar will work with any gauge strings in any tuning." A proper setup means that from nut height to intonation adjustment to string height, EVERYTHING is set up PERFECTLY. As long as you don't have any hardware problems, you can set up a guitar for any tuning with any gauge strings. There is nothing special about standard tuning that means guitars only work with that. It's just a tuning. Pick your tuning, pick your gauge, and set your guitar up for it. If it won't cooperate, you have a crappy guitar. End of story.
So what you mean is that the bridge was wonky? I've also seen many guitars with the bridges in the wrong place, ESPECIALLY Jacksons (their lowest-end imports SUCK). I know what an out of place bridge looks like, and if you have one you'll know it to. The recessed routing for the tremolo (we're dealing with a Floyd Rose here, remember? Not a ToM Gibson) makes it pretty damn obvious when something is in the wrong spot.
And you're clearly a bigger jerk the more you post. I'll explain it like this. A FLOYD ROSE IS NOT A TUNE-O-MATIC. The string has a much longer contact area with the saddle than there is on a ToM. The area where the string breaks over the saddle eventually wears away, especially under heavy trem use. It's just like getting a false overtone from a nut. You have experienced that, right? Where the front edge of the nut is either cut wrong or has worn away so it produces an overtone? It's the exact same principle, and it WILL screw up the intonation.
Ummm.. did you not see where he said he used fairly high action? Are you not aware that high action does wonders to mask low frets? Do YOU have any clue what you're talking about? How could a 12th fret be lower? Umm... maybe it was ALWAYS LIKE THAT? Maybe it's worn down? Since he uses high action, the whole area around the 12th fret could use being refretted and he doesn't even know it. One of my guitars is like this. How could this affect the intonation? Seriously, you have to ask this? You have no clue how a low fret could cause intonation to be off? How about this. Low fret = virtual higher action. It may not be much, but it doesn't take much for the note to ring sharp. Also, it's nice to see that because you've never seen it that it doesn't exist. Unfortunately, I have seen it many times and know otherwise.
And I'm sick of jackasses acting like since they read the StewMac book, and have worked on a few Gibsons, they know everything. I'll tell you right now, I don't know everything. But I know Jacksons. I spent a while working for Jackson as a QC tech (right before Fender bought them), doing setups on all the guitars before they went out to the dealers. I also handled a fair amount of the warranty repairs. In my time there I estimate I handled between 7,000-8,000 Jacksons of all makes, models, points of origin, and color. I had two of the best techs you'll ever see (Kevin Easton and Reid Rogers) as my instructors, coworkers, and friends.
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BTW, I've seen your site and know your work and know that you know your ****. You've just overextended yourself trying to make me look like a moron.