Here's another that just happened to me today! So my main guitar that I've been recording my new album with has been driving me insane. I've been working on everything from crowning frets, truss rod removal and adjustment, new saddles, new springs for the Floyd, new saddle lock blocks....it's been a nightmare.
Last night I finished everything up and am astonished at how awesome my guitar sounds and plays. It's back to itself...with one weird thing....a bit of a mid range push that I never had before. Now granted, with that much work, action, truss, Floyd etc...you are NEVER going to get the same sound you had. You'll come close...but chances are there will always be something missing. Well, the perfectionist that I am, I had to figure out what was different.
After some trial and error, the major tone change came from....get this....the pups being adjusted too high to the strings! I had forgotten to adjust the pup height. As soon as I moved it away from the strings, the added mid range boost I was puzzled about, disappeared. I'm not one that likes my pups nearly touching the strings like some people do. Mine are usually right in between. But these particular pups are powerful...so I usually have them set more "into the body" so to speak. The adjustment instantly cured my little mid range anomaly.
This is another thing with modeling that I've noticed. Any little changes to your guitar can drastically effect how your tone sounds. Even a string company change with the same gauge strings can alter your tone....that was my other issue. My GHS order was a little late (I get a case of Boomers per month...I know, you guys hate them. LOL!) and I put a set of Ernie Ball on. Sound was good, but something was missing.
So though we have the best of all worlds with our incredible, magical black box, it's a very spoiled box. Sometimes sounds I've created with one guitar REALLY sound different when I use another. Other times, the same sound works great. Finicky black box we have...but I'd not change it for anything.