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Fixing a weak Low E on a 32" Scale.

Here are some things to check:

Neck relief correct
Nut height correct
Quality of the nut slot (taper etc.)
Pressure on the nut (winding on tuning peg)
Witness points set
String not defective
Bridge height correct
Bridge saddle makes solid contact
No high frets ahead of problem area
 
So after I tweaked the pickups, it’s only the open E that’s a problem.

I gave the thing a decent setup when I got it but not any nut or fret filing. It plays very smooth, no buzz, and the neck is quite flat.

Nut issue sounds likely.
 
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So after I tweaked the pickups, it’s only the open E that’s a problem.

I gave the thing a decent setup when I got it but not any nut or fret filing. It plays very smooth, no buzz, and the neck is quite flat.

Nut issue sounds likely.
In case you didn't think of this already: Possibly, the break angle over the nut is too shallow. You can rule it out by pressing down a bit on the string behind the nut (between the tuning peg and the nut).

Typically, based on TB postings, the pickups may be 'anemic', otherwise, Aerodynes enjoy a very good reputation. Enjoy!
 
This may have absolutely nothing to do with your situation but IME in receiving new instruments and setting them up while working in music stores since 1978, I have learned to check and tighten everything you can possibly think of. Who knows? One of the most common loose parts are anything related to the tuning machines. As instruments change locale they can shrink enough to cause loose parts. This has been only an observation of mine and not meant to be a definite cure but something to think about.
 
It sounded fine with the strings it shipped with and with ernie ball brite flats. I just really like chromes and was hoping to make them work.

I think you may have just answered your own question....is it the Chromes? You may have a defective string. Or, your particular bass may not respond well to the higher tension Chromes. I like Chromes too, but have had (and still have) a couple basses that don't sound right with them, which surprised me. Nothing scientific here, but I think it's a resonance thing, suspect the tension may trigger it on certain basses.

Another (kinda pricey) approach to getting more authority from the lowest notes is a set of Pyramid flats. The 105 E string puts out a massive fundamental, to the point where it seems to be a mismatch to the other strings. But like the manufacturer says "it's not a bug, it's a feature".
 
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A couple thoughts… what’s the amplifier situation? Is it possible fundamentals are missing their overtones? How does it sound in a mix?

Since we’re talking jazz setup could it be that both pickups are on 100%? Maybe cut the bridge pickup volume to 80-90% to eliminate the scoop effect?

Is the E string kink damaged? (Do Chromes have that?). And not kinked before winding?

First D'Addario Chromes Try: DEAD E-string???
 
You said they are Medium GAUGE strings - are they Medium SCALE strings? If you are trying to use long scale strings on a medium scale bass the tension will to totally wrong for them and they will be muddy. Strings are wound at the proper tension.

You should be using the ECB81M set.
 
You said they are Medium GAUGE strings - are they Medium SCALE strings? If you are trying to use long scale strings on a medium scale bass the tension will to totally wrong for them and they will be muddy. Strings are wound at the proper tension.

You should be using the ECB81M set.

I always use regular long scale strings on my 32”. Never any problems. I don’t think it is really necessary to use medium scale strings.
 
You said they are Medium GAUGE strings - are they Medium SCALE strings? If you are trying to use long scale strings on a medium scale bass the tension will to totally wrong for them and they will be muddy. Strings are wound at the proper tension.

You should be using the ECB81M set.

These are heavier than the only medium scale set of chromes, so no, they’re not muddy. Part of the point of medium scale is that I can use heavier strings at lighter tension.
 
I've encountered something similar and will agree with others who said that this is most likely a resonance issue inherent to the bass. Flatwounds will emphasize this sort of phenomenon because of their big low fundamental and relative lack of certain harmonic overtones. With roundwounds, it may very well not be as noticeable.
Dead-spots commonly found around frets 5-7 on the G string are also resonance issues, for which Fender has developed the "fatfinger", which may help with your weak E as well, but you won't know until you give it a try.