You can only get a little bit north before you hit flooding. In January we went in with a small inflatable and found that the mine does indeed continue the full length of the west quarry and turn the corner at the top. The last time I looked properly in the west quarry, which was a while ago, I couldn't see any ways in, but there were a few bits that looked as if they might open themselves up, you can certainly see all the backfilled adits from the inside.
I'd love to be proved wrong but I'm almost certain that the only underground activity in Charlestown is what we've already seen. The quarries are, as you say, extensive but I'm pretty sure they are all above ground. None of the various sources I have checked have so much as hinted at any other mines there. It hasn't stopped me looking for them though.