so my low e string reverbs louder than i pick it, someone told me this was a intonation problem but i checked it and its fine. Any ideas on what my be causing this?
more info: its like a half second reverb after its plucked, the second reverb being louder than the first and then it goes down, and it gets worse the higher on the low e I fret.
Thanks for the help.

Pickups too high on the bass side, I reckon.

Made worse when you fret that string higher up the board and therefore push the string further down towards the pickups.

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Welcome.

Premising there is absolutely nothing wrong with your string and that its nut slot is properly cut, it sounds like you have, "Stratitis".

With the guitar on your lap, using both hands, slowly press all the strings down at the same time until they all are touching their respective polepieces on all three pickups and then gradually and evenly relieve your hands pressure until the strings are back to their normal position. What you are doing here is synchronizing the magnetic flux of the pickups. If this doesn't work, then one or more of your pickups on the bass side is/are to close to the low E string and is/are literally sucking the string in to where you'll get all sorts of crazy overtones like you've mentioned.

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You dig?

i tried the pressing down thing to no avail, ill try a pickup adjust tomorrow and hopefully itll work. thanks for the help yall.

i lowered the pickups on the bass side quite a bit, to no avail. should i lower them almost into the guitar? like as low as they can go? or take it to a shop and get them to look at it?

Raise your E string at the saddle

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so it ended up being a problem with the neck tilt. However, the noise is still there, and the guy who fixed it said its a typical strat thing caused by the tremolo, is that true?

No I've never come across sympathetic trem spring resonance. I thought I have a few times but it was always cured by something else. Usually action or pickup height. If you think about it, your pickup has to be operating upside down for it to happen. It's certainly not the string vibrating through it to any appreciable degree. If that was the case, you'd have to apply way more tension to each string to reach concert pitch. The talk length of the string would be increased by the length of the spring and the block.

Best thing you can do with the neck tilt is back it all the way off. Get the neck tight then do the screw up just enough to put a slight bit of pressure on the neck and stop the screw rattling around.
It's the most useless thing I've ever seen on a guitar ever. If your neck needs re seating to a different angle. The only real way to do it is with a shim.

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I really appreciate the help, but can you provide a sort of step by step, im still a bit new.

In what? Setting up the guitar?

In truth all I can do is give you a few pointers and a basic order of what needs to be done, and I'm more than happy to do so. You'll have to do all the leg work though.

The first thing you need to do is get the set to factory spec. Undo any microtilt adjustment you may have made then with the guitar tuned to concert pitch (or whatever you tune to) and set the neck relief.

To do that put a capo on the 1st fret, press the 21st/22nd fret high E string and measure the distance between the top of the 8th fret and the underside of the high E string.
With a set of .009" strings your aiming for that measurement to be around .012". With heavier or lighter gauges you will need more relief as the string either travels further when vibrating (lower gauge). Or takes up more room, through being bigger (higher gauge).

So how does the relief measure up, before we go onto either adjusting that, or the next step?

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the shop i took it to set the neck relief, intonation, and gave it a full setup check. i just need to know about finding what it is that is still causing the strange string vibration.

Yeah and thats the only way I can determine what is causing it without putting a hand on the guitar. You need to set the thing back to Fender spec's, not some shop tech's idea of a setup.

There are good and bad techs all over the world. I personaly don't trust one who doesn't spend a bit of time watching the customer play the guitar. Or returns it with a fault and no explanation of it's cause.

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gotcha, well ill set the truss rod to default specs.

on the high e string i would say its a little less than 1mm.

ok, on the 1st string, high e, its a little less than 1 mm, and on the low e (pitch wise) it is 1mm. which is the fender websites standard.
also, i tried lowering the pickups by quite a bit, and there was no alteration in the how it is acting. Could it possibly be a strange tremolo noise?