Upgrade to IOS 5 problems

When I try to upgrade my iPad 64GB-3G to IOS 5 I face 2 major issues:
1)  I need to upgrade using the computer I sync with:
     This computer is a Windows with limited C: drive (I use partitions to separate data/media from programs and OS), and it doesn't have enough
     free disk space for proper backup of my iPad.
     There seems no way to specify where to make the backup. Not everyone will have 64GB free disk space on the C: drive.
     How to solve this dilemma? It should be possibel to select a backup drive/disk . . .  Why doesn't Apple solve such problem?
2)  If I try to upgrade using my clean MacBook, I get warning that I will loose all data (content: own made doc's, datafiles for all kinf of apps,
     photo's in iPhoto, books in iBooks, . . ); I would expect a backup possibility of all apps with settings and related datafiles.
     In the past I also had problem with issue 1) and then I used my sun's Mac to upgrade to IOS 4.2 and lost no apps or datafiles.
     So it seems this IOS5 upgrade has much more consequences and this should be more clearly stated in upgrade documentation . . .
3)  How can I backup all my datafiles eg. I made two Numbers spreadsheet, but don't see them in iTunes as datafiles belonging to numbers.
     Is the only way to get them off or back them up using e-mailing to myself (using Google) ?
     I don't care about apps or OS, but my own data I create is "holy" and I don't want to loose it. Apple people, can you please help me?

apple surely has the worm eating at it's core with this glitch... I have the same problem, can't upgrade because of insufficient available backup space on the original drive even though all my music and media is in a second huge empty drive. Why can't apple simply let you specify where to backup your ipad bewilders me! they really need to fix this quick because this is a huge boo boo on their end.

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