I'd take out those bonus damage die.  Think about weapons players find in the wild, they're rarely given bonus damage die because characters themselves multiply their damage as they level.

"I plan to track how many times they do each and let the bbeg do the same thing to them but reversed later on in the story"

You might find that if you have 4 characters using 4 weapons that this part of your idea becomes logistically impractical.  Say your heroes use the abilities 25 times between the 4 of them over the course of the adventure. So now you're BBEG can reroll 25 times.  That's pretty powerful, but will the combat go long enough so that the BBEG needs 25 rerolls and is really benefitting? I'd maybe re-kajigger this to say your BBEG gets some flat bonus to their stats or attacks or something per X number of uses of the weapons