Ahh!  No wonder I never liked these.  I put quite a bit of effort into getting rid of that resonance peak, tried every trick I know for killing enclosure resonance except the holes in the cups.  In the end I believe it is coming from the driver.  I think the YH100 is kind of the Tesla Yamaha.  AFAIK it is a YH1 driver with stronger magnets, making it more efficient.  The plus side is astoundingly good bass capability, close to LCD-2 I'd say with the right damping scheme.  And it has a slightly faster sound than the YH1 either that or the peak gives it a "clarity effect" or maybe both.  But I think what we're seeing is possibly the diaphragm being driven too hard by this increase in magnet strength.  The YH1/HP1 was developed first, and I bet they didn't do their homework as much when making this model, but instead kind of hacked a new flagship by making the HP1 magnet stronger.  (This was their flagship after the YH/HP1000). 

I actually think a lot of people would love these phones, and a lot of people do.  The ringing and peak gives electric guitars a rather Grado like bite, but the rest of the signature is more balanced and they have crazy man bass that will shake your skull.  Doesn't have to be emphasized, it just goes very deep with a lot of control. 

Will be interesting if Purrin does distortion to see if distortion is improved from the YH1 by the stronger magents. 

This pair is modded in a similar fashion to the YH1 but with no holes in the cups, but after spending a lot of time on them, I eventually just sent them in.  Nothing I did changed this resonant spot, even when I focus on nothing but resonance killing, it's still there.  That's when I gave up and sent them in to see what it would look like. 

That 2-3k region is certainly a problem area with certain yammies. I have usually found the smaller driver yammies to be better behaved in this regard.

Although, I don't believe that yamaha slapped higher strength magnets on HP-1 to create a YH-100(That freak is called aniso HP-1 :p)
The Aniso HP-1 and YH-100 have similar magnet strength & despite that they sound quite different from each other(still have the yamaha house sound though).Also the efficiency is different,so I surmise that their  are some driver trace differences as well between HP-1 & YH-100.

RD : Are both of these damped with felt?

RD do you think it's a bigger PIA to mod the YH-100 since they don't have the rear opening holes like the HP-1?

3kHz, humm, difficult question because pretty much everything could potential ring there (closed or semi-open acoustic chamber, diaphragm, frame, coupled structural/acoustic mode).

Without seeing the actual design, the quickest way to investigate would be to measure the open air baffled (doesn't need a large baffle, just stick the mic in the near field) driver response. I am not familiar with orthos in general, and the yammy driver in particular so I am close to useless here .