please help me troubleshoot my build

Now you have another reason to change them :)

I ordered a length of generic silicone tubing rather than the pricier pre-cut Fender-branded rubber tubes. I went with silicone because it won't deteriorate over time and gum up like rubber does. Should be here in a few days.

Meanwhile, and again this might be purely psychological, but i noticed that if the guitar had just been taken out of its case and is cold (well, not warmed up yet), the beating is really obvious. But after warming up the strings and the bridge -- i lay my right hand palm on the saddles and run my left hand up and down the neck for a minute or so -- the beating becomes quite subdued, such that proper muting of the strings and judicious vibrato covers up the beating quite well on long notes! :unsure:
 
I urge you to check:
That your string is not impeded
Have you rockered your frets?
Make sure nothing is allowing sympathetic vibrations (loose items)

As you know this is not normal. So you have to find what is not normal.

You weren’t clear if you changed the strings.
 
This is most likely NOT your situation, but as an illustration of how to proceed

An acoustic friend of min suddenly started getting ghost notes on certain strings. I checked nut height and rockered the frets. All good. As I was preparing to see if the bridge plate was loose, I found that 3 strings were “indented on the underside “. Yep new strings fixed it. Turns out the guitar had a fall against an item at that location. The strings became dented rather than the frets. A much cheaper solution in his case.
 
I urge you to check:
That your string is not impeded
Have you rockered your frets?
Make sure nothing is allowing sympathetic vibrations (loose items)

As you know this is not normal. So you have to find what is not normal.

You weren’t clear if you changed the strings.

Yes i still have your suggestion re: new strings in mind. No, i have not replaced the strings yet as i haven't gotten the chance to buy new ones.

I'm working on the sympathetic vibrations part, hence buying silicone tubing to replace the pickup height springs with.

At the moment i don't have a fret rocker, but my action is not exactly low. I can see good clearance over the higher frets when fretting the affected notes. The affected notes also sustain well and don't choke.

Thank you for the tips. What else can i check?
 
Have you tried taking the guitar to a friends house and seeing what happens there?
Again to me it sounds like there's something loose, you hit the string and you're getting a sympathetic vibration ... and yes change strings, stuff in foam, raise your strings to a ridiculous level .... try everything .... or bring it to a pro. Where do you live maybe someone here can suggest a good luthier.
 
Sorry guys, i'm giving up on this guitar. I replaced the pickup height springs with silicone tubing but that didn't help with the beating. In the process i was careless and while unscrewing the middle pickup, i let go of it and it slid towards the bridge pickup (i was holding the pickguard at an angle). They both stuck for a few seconds before i noticed and quickly removed the middle pickup. When i put everything back together, the middle pickup (a Dimarzio Chopper, normally a loud pickup) sounded really weak. The bridge pickup sounded brighter (thinner) as well. I must have demagnetized both pickups. I'm frustrated and sad and angry at myself and i'm putting this guitar away for now.
 
Well I hate to hear this, but putting it aside for a bit may be the best thing. There were a number of things suggested that I am not sure you checked. As an example, rockering frets. I don't care how high your action is, if you have a high fret, that can only be realized by measuring against adjacent frets. Action doesn't come into play on this.

Also, you never truly checked for string impedence other than eyeballing it.
 
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