Bo,
It does not sound good from what you are saying. It sounds like you cooked the Yamaha and the Peavey has gotten hot enough to warp the voice coil and its scraping in the "gap".
Depending on the SP 118s that you have, you may be well over the threshold for power if you are continuously clipping the 2450. You are sending a solid 1,200 watts per speaker in the current configuration.
1. How often are the red clip lights coming on?
If Steadily, then you need to back WAY off.
2. You may want to consider replacing both of your Black Widow drivers to some more powerful drivers. Peavey offers stronger drivers but this will not fix your need for more bass. If you find yourself clipping the amp constantly then you need more subs.
For the time being I would suggest at least replacing the basket of your damaged Black Widow and watching the level very carefully since you are over the recommended power level for those speakers to start with, much less at full tilt from the amp. Consider upgrading to higher powered drivers (I think the newest driver is the "Pro Rider" which holds more power than the older Black Widows). If you swap out to upgraded drivers in both, you will still have a spare replacement to work with in case.