You just brought up several things that would cause me to drop those speakers, fast.
Whatever Mod the previous owner did, you likely won't be able to confirm if he modded the XO as well. Chances of dropping a tweeter into an existing speaker and having a perfect match to the TS Parameters, thus performance, is like playing the lottery.
Without some extensive research I would not attempt such a mod... and I'm learning speaker design. One pair of speakers I purchased was a modded kit from PE... and I am currently performing a new mod with the guidance of the designer who modded the kit in the first place. This includes me rebuilding his XOs too!
That, coupled with your experience setting them up in your room tells me something is wonky because they should just work if all is correct. (Room acoustics, aside, that is.)
Regardless:
The reason I thought Bi-Amping might help is because my understanding of Bi-Amping is that it bypasses the internal crossover of the tower and instead relies on the crossover of the yamaha receiver
This assumption is wrong. You are feeding the Low and High sections of the
existing Passive XO the same "Full" signal as sent from the AVR. The existing Passive XO still has to process the separate Bands for the respective Drivers: the Low Pass Filter on the Woofer Circuit is still working the same as if you were just Single Amping the speaker, same as the High Pass Filter works for the Mids and Highs.
Yours may be 2.5-way, which still will work similarly in that the tweeter will be on its own circuit, and all the woofers, including the.5-way will be on a separate circuit. (My guess only, since I am unfamiliar with that speaker.)
That said, what could be happening is that the Replacement Tweeter and the .5-way woofer are not well matched, AND/OR that the XO was not adequately redesigned. Neither wins anything other than a failing grade.
My vote is new for new speakers.
You cannot Bi-Amp your way out of problems, be it room acoustics, Sound Quality, or bad speaker design.
Cheers,
R