Without more information, and this is merely a guess, it seems that you may have lost some of the midrange drivers, or more in your loudspeakers, as the surge could have passed through the amp then into the speakers.
Amplifiers usually just blow a fuse, or stop working rather than becoming less clear with less apparent power. The clues for this seem to be, "harsher,(less midrange information--less volume)--'continuous drone' implying, again, less midrange information. 'Muddy and unclear'--this all sounds as if you may have damage in the speakers. I have seen this happen on numerous occassions.
Quick test--gently, gently press on the midrange drivers and listen for a 'scraping sound'(do this with no signal going to the speakers).
Let's try to get a qualified tech to come over and check all the system for lightening damage.
Thermal stress can take out parts of a system, now and or later. If you will let me know where you're located, I can try to contact a local dealer for you if I have one in your area. (Your homeowner's insurance should pay the dealer for a service call--to inspect your whole system). If you'll give me more info by private email, I will try to move this forward. email@example.com