Wow, you have a lot of issues........
First off, you listed all peak power figures, which are meaningless. RMS power is the only thing that matters
Second, that headunit is probably only putting out 10-15 watts per channel, so the crackling is either the crappy amp inside the headunit, or the speakers have an issue. My guess is that there is no highpass on the speakers, so you are pushing them beyond their limits by making them try to play bass also, mixed with the crappy internal amp causing the crackling problems.
Third, it sounds like the subs are wired to the "rears" on the deck, which is why the fading effects it like it does. I'm going to guess that your deck doesn't have sub outs, and might not have more than rear outputs, so you may just have to live with the bass fading issue.