I get a disk error when trying to upgrade to mountain lion on my mac book pro that also runs bootcamp

I recently tried to upgrade my macbook pro OSX to mountain lion via the app store. When it tried to install it gives me a disk error. I have run disk utilities and repaired, verified etc. but it makes no difference. I am running bootcamp as well and have tried to modifiy the partition sizes in disk utilities, but it says for both that they cannot be modified. I can switch my startup disk and reboot in windows, no problem, so getting my files off isnt the issue. I have also tried to recover the hard disk using time machine which i was lucky enough to backup the day before it all went wrong. However, time machine runs fine until it asks me which disk to recover and it gives me an option of the time machine disk or bootcamp, but no option for my mac partition. So, I have tried everything that makes snese, but getting errors with disks lock, cant repartition, disk error needs repair (which i know is not true, its only because of the Mountain Lion OSX that its messed up). Any ideas?

You have some other problem with your boot drive that has corrupted data backed up to the TimeMacine drive.
My advice is to boot into each operating system and manually backup just your Users files each to separate regular external drives (no Timemachine or backup software) and disconnect.
Make a note of any serial numbers, emails, address book contacts, export bookmarks etc. that isn't typically in your users folders data.
You might be able to Winclone 3 the Windows as a whole thing as it's appearing not to have issues but it's your MacintoshHD partition that is so that will have to be rebuilt from scratch.
Most commonly used backup methods
If your OS X parititon doesn't boot, you can use this to recover files.
Create a data recovery/undelete external boot drive
Without any further detail about your machine I can't advise specifically what to do, but it involves using Disk Utility to Zero Erase (move slider one spot to the right or in 10.6 using Security Option) the ENTIRE boot drive and reformatting, then installing OSX fresh and then setting up BootCamp again.
If you wish to switch your boot drive for something better, this is a good time to do this.
Install/upgrade RAM or storage drive in Mac's
If your machine is capable of Internet Recovery, then use that, then upgrade.
If your machine came with 10.6 or earlier, then use the 10.6 install disks and work up from there.
Erase, formatting, OS X installs on Mac's

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