The QC thing is very odd. I recommend asking them exactly what they
mean by it. It's possible they assume you will contract out the timing
and therefore that person will do QC, but that still seems like an odd
way to ask you about it if so.
As for how to charge for this work, you need two different rates here:
a rate for your translation, and a rate for the timing/typesetting. If
they want you to do both, then you add the two, or if you feel like
giving them a package discount, that is up to you. But know exactly
how much you're willing to translate for and how much you're willing
to time for. Don't just have one amorphous rate; the two activities
are totally different, they require totally different skills, and they
are worth different things.
To answer your question about charging by line, it is not customary to
charge by line. Charge by minute of video.
Incidentally, it also makes me concerned when anyone (translator or
not) talks about "script translation" of anime. There is no such thing
as a script translation. You translate the audio and video, not the
script. The script is merely a reference for you, and at any given
point may or may not have anything to do with what is happening
onscreen. As someone who works in anime translation QC, it is very
obvious when someone relies too much on the script. Just my $0.02
worth of free advice...
Alys @ hope that helps