Well I spoke to my ISP and they confirmed what a lot of others had found, that it's due to Sega's servers being blacklisted by backbone providers as a result of the DDoS and that it's a case of waiting for them to be unblocked again which could range from days to months.
After that I decided to just bite the bullet and go for it, there is a (potentially) free (but rather complicated) method posted on PSO-World that lets you play the game, doesn't trigger the e-mail requiring you to confirm your identity to unlock your account and has a static Japanese IP.
http://www.pso-world.com/forums/showthread.php?t=220299
Not going to make any guarantees that it is totally safe since Sega's actions are about as predictable as a random number generator, but it let me log on and play perfectly earlier today and people haven't reported any issues so far. I'd assume as long as you are sensible and don't try to log on from that JP IP and one from another country in a short space of time it'll just look to Sega like you are now in Japan but still using the same PC.