To answer one of your questions. Yes, changing speakers can create very dramatic changes. Speakers account for the majority of how your sound, well..... sounds. The room itself is also key but I'm guessing you had no dramatic changes in that regards.
Speakers that follow different design philosophies can sound very different. Companies that follow similar design philosophies can also sound very similar. However, your change began with a new AVR.
Some people will tell you that different AVRs will change your sound. Others will tell you that AVRs of decent quality and powered to your needs will sound the same. I won't start up that argument here, but I think it's safe to say that even those who feel AVRs/Amps can make a difference would say that it's probably not as big a difference as you seem to be describing.
NO working AVR, without settings maxxed to extremities, should be so shrill that you have to disconnect tweeters.
My guesses, and that's all they can be
-- As mentioned. the new AVR is using a sound mode or setting that needs to be changed or turned off. I personally have yet to hear a DSP sound mode (stadium, jazz club, rock, etc.) that I like. Start with everything natural and then tweak from there.
-- The old AVR was using a sound mode or setting that you were very accustomed to that you haven't replicated yet.
-- It has a technical issue (broken). I'd try looking up how you reset it to it's factory defaults then try it again. If it's upgradable, look for upgrades or patches and apply those (after the reset).
Borrowing another AVR and making sure that they are both on natural settings for testing purposes, should give you a very clear clue here. Even if you believe one amp can sound better than another, there definitely should not be so much difference you feel compelled to hack up your speakers by removing the tweeter. If that is the case, return the Yamaha like the first buyer obviously did if it's an open box purchase.
-- The speakers developed a technical issue. I'm not accusing but it's human nature to crank up the volume when trying out new equipment. It's possible drivers or were damaged or the crossover electronics. That would be odd and I know little of how they tend to break down, but I would assume that electronically it would be possible for a capacitor or resistor malfunction and distort the signal or (although less likely) that something could actually melt in such a way it creates a short resulting in way too much signal is being sent to the tweeters. Someone more knowledgeable can comment there.
Did you try listening to just one speaker at a time, swapping left & right? A visual inspection of the drivers and crossover could also provide clues.
Sorry for the long post. I'll end it here as I have run out of free (oops I mean, lengthy conference call time.)
