Recovering my Mac multiboot setup

I'm still not at all clear on why my HDD in the Mac became unworkable and unfixable. It seems something very serious had happened to the OS X partition (90 GB). The AppleCare guys pointed to the directory structure as having been damaged and they pointed (although reservedly) to using both Grub and EFI as bootloaders on the same HDD as both will be stored in the very same place. This, then, means that the MBR (which is where Grub sits) is in the EFI partition. Hmmm..
But if this is true, then I'm going to have more problems as I'm unlikely to stay away from what I'm doing unless I get incontrovertible evidence that it's unworkable. But it has worked fine for a year with no problems until this one.

I got the following articles from the AppleCare guys which were supposed to help me fix the problem.

In any event, once I had completely erased the whole HDD, everything started working as it should. OS X install was a piece of cake and it's fully receovered now with all of my stuff back. It's great to not see those annoying sudo errors and have Visor start normally.

Ubuntu install went fine without problems although I don't have everything fully back yet but it's only a matter of time.
Foresight, on the other hand is problematic. Perhaps its because the version I installed was a bit old (2.0.2) and there was an awfi=ul lot of updates. Maybe I'll download the latest version (2.0.4) and try again with that tomorrow.
I had two problems:
1. Yakuake, although it installed normally, will only work as root. A lot of stuff in ~/.kde had root as owner. I changed this to my user but didn't improve matters. Sounds like a similar problem I had with Intrepid (Ubuntu) which got resolved when I installed a bunch of updates.
Funny thing is that when I type yakuake in a terminal (without sudo), it just stays open with no errors or any other comments. If I ctrl-c this and type sudo yakuake, it errors (communication error--it probably crashed) but yet, yakuake starts and is fully usable but as root.
2. The Desktop icons dissappeared and I can't get them back. Going to Places>>Home Folder opens nothing.
I'm very inclined to blame the huge amount of updates so I'll start afresh tomorrow.