Did you reverse the connections on the old woofer and have the noise go away?
Did you check the woofer in the other cabinet to make sure it is connected the same way as the new woofer?
If the woofers are wired oppositely you will get out-of-phase bass which will have a big effect on the sound, especially if these are 2-way type speakers.
You will also affect the sound negatively if the woofers are wired in a way which is the reverse of what the design engineer intended, in relation to the tweeter.
However, if you blew both tweeters out at the same time as you nearly fried the woofer, then there should be no problem, assuming the speakers are 2-way types.
Anyway, if the new woofer is just a generic replacement woofer and not an exact duplicate this is all academic and we are not really on the same page.
