I have a myriad of problems with my guitar I built, but one that I noticed right away was the LOW E string seems to sound slightly muted.

The Nut slot on the neck I baught seems to be for like a 42 gauge string and I used 46s, 48s, and 50s for my bottom, and the LOW E doesnt quite drop all the way into the slot.

I noticed this LOW string sounds kind of muted no matter which fret im playing it on. Could the nut still be responsible for this?
Fretting means the nut is out of the equation now. Check to see if the string clearance is good across all the frets and pickups. That or it could either be the saddle or you just got a dud string. It happens. What kind of build is it? Pics?
Gibson RD Silverburst w/ Lace Dissonant Aggressors (SOLD)
Electra Omega Prime Ceruse
Fender Franken-Jag Bass

Amps and the like:
Laney VH100R
Seismic Luke 2x12
Dunlop 105Q Wah
Gojira FX 808
Line 6 M9
Ive tried changing the strings, I changed the tremolo, the saddles, I tried adjusting the pole pieces, it still sounds slightly muted. Maybe these duncan ssl1s have a scooped low end or? idk

I baught a precut stratocaster wood piece online on ebay, I dyed and layered it myself, the neck I bought from the Stratosphere bay store the guy disassembles fender parts and sells them individually for higher prices i bought a one piece maple neck with 6105 stainless steel fretwire, its very tall and the saddles are basically maxed out to compensate for that,

I bought Duncan SSL1 single coil pickups from a guy online and i wired them in myself and they have a little ssl1 sticker on the back so i assume theyre legit i really dont know but they sound great except this e string.

I would take this to a professional and get some of these things worked out except that im broke after spending all my money on building the guitar lol maybe in a couple months ill take it to a guy if i can find a guy i trust