Hey. I remember from my early mess-up days that knowing the hdtoolbox parameters will fix that - assuming it is an rdb-problem. If you have several partitions it is probably kind of hard to guess, but if you only have one, just max out the disksize in hdtoolbox, save your settings and reboot. You should not be able to do any more damage than done already, should you mess up.
Oh, and if the harddrive does not show up in hdtoolbox, you have a hardware problem somewhere. If it shows up with the correct parameters (not default ones, like I assumed above) it should work just fine (but clrealy does not).
Finally I have no idea if it works above the 4gb limit either, but as said, it should not harm anything further.
Sincerely,
-Kenneth Straarup.