So, the only caps that I changed are the output coupling caps: I started with the stock .1 caps but quickly went to .022 to tame the bass.
From what I can remember: I started noticing this "resonance" issue after installing a new O.T., I was trying to reduce bass and wondered if a different o.t. would help. The new o.t. didn't do much and so I went back to the stock o.t. and started noticing a louder D4 note.
After some time the amp started producing a loud crackling sound, not always, sort of an intermittent issue. By tapping with a wooden stick I noticed that the taps were amplfied when tapping on the power tubes cathode resistor; tapping on it would also make the power tubes flash... I replaced the cathode resistor and the crackle went away for good.
But, that's when I noticed the resonance issue: not only the D note is louder, B, Eb and E are noticeably louder.
In a situation like this, what are the things you would check in the circuit? It would be helpful to know where to start...
Speakers can do that ...
... it is not a guitar problem. ...
I've never noticed that with my 5E3. Nor have I ever heard of this particular problem. Maybe a better starting point would be to use original values for coupling caps and reevaluate the sound.
... check for any poor solder contacts. Tap on the pre-amp tubes, if excessive noise try replacing that tube.
Quoting a whole bunch of stuff, because:
- There's no "place in the circuit" to target individual notes unless you have a parametric or graphic EQ.
- Most guitar amp circuits (and certainly the 5E3 Deluxe) can shave the bottom, shave the top, or scoop the middle. And a 5E3 lacks a Fender blackface tone stack "scooping the middle". So there's nowhere to turn to tame individual notes as you requested.
- Depending on where you set the Tone control (and which channel you're using), the 5E3 Deluxe can have a measurably "flat" frequency response... which then sounds like "too much mids" to many players who are used to other amps whose tone stack scoop a bunch of mid. That fact can then make other flaws of the guitar stand out.
- That tapping produced crackling sounds, flashes of light, etc, sounds like there could be intermittent connections in the amp. As in poor solder joints. If "some notes jump out" that makes me wonder if vibration sometimes temporarily corrects a "poor connection" making the note louder.
- Speakers are the thing that have a bunch of peaks & dips. When "some notes jump out" it is often about the speaker's peaks. However, those peaks/dips are usually up around 1-5kHz and way above the notes you're describing (more like harmonics of the notes you mention). Though sometimes we might notice one speaker has a lot more "low-mid" than another.
- A stock 5E3 is fine except I would agree it could tolerate rolling off some bass; and some folks won't be used to how much midrange it has. I'd suggest going back to the stock circuit then re-evaluating as Sluckey said. "Weird resonances" at that point are not the circuit, but the guitar, or the speaker, or intermittent wiring.