Clone external drive to internal drive...

Hi there guys,
My iMac was working perfectly yesterday, but for some reason, iDisk isn' t syncing now. At all. I have repaired permissions, trashed pref files, disabled syncing, enabled syncing, set up new user accounts etc etc, but the only thing that worked was when I booted from external - it synced just fine.
I want to know whether it's worth moving the external over to the internal and copying things over from there/cloning the internal from my FW external?
Or should I just boot up from external for the forseeable future?
I made a partition on my external and created a bootable clone on a partition with 1GB more space on it than the internal.
The internal shows 97.8 GB (105,020,411,904 Bytes) are used, but the external shows only 86.6 GB (92,987,826,176 Bytes) used and it's supposed to be a clone!
The Internal has a size of 148.9 GB (159,907,630,080 Bytes) yet the external has a size of 149.9 GB (160,927,055,872 Bytes) so obviously I worry that if I clone the external over to the internal, that it might not fit.
Also, I use SuperDuper!. Would I have to erase the internal drive before I started to clone it from the external?
Is there anything else I can do to save the iDisk syncing? It works just fine on my other iMac and my MacBook (which uses the same router).
Thanks.

Solved.
Booted up from external. Cloned internal to match external. Booted from internal. Done.

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