Windows – Sharing Drive Between Ubuntu and Windows 7

It's certainly possible to infect Windows through Ubuntu. It can happen if you have an infected file that gets transferred from one OS to the other; however, an infected file that lives only on the Linux partition will probably not have any affect on the Windows OS.

The easiest way to keep Windows clean is to use an antivirus application in Windows. It might be a bit overkill to also install an antivirus app in Ubuntu as well; however, if you want, you could use something like ClamAV to scan files before transferring them to Windows. There's more info on ClamAV in this question on SuperUser.

The good thing about ClamAV is that it's an on-demand scanner, so it doesn't consume any resources when you don't need it. That way, when you transfer files from Ubuntu to Windows, all you need to do is scan them before copying them over to the other OS.

A1 -> merge it to make A1+B1.
A2 -> NTFS
B2 -> Can bring it down to ~ 40 GB, allocate remaining to A2.
That would be my recommendation.

as I read NTFS does not work nice with permission

I'm not sure what you mean by this ?

1) format the data partition to ext2/3/4 and move my home folder from linux there, and get a driver to read ext partitions in windows 7.

Not recommended, especially since you don't want a read-only file system.

http://www.fs-driver.org/ looks promising, but I'm not sure how it works with ext4 and windows 7 (not officially supported, when trying in vista compatibility mode, it tells me I need to format the ext drive to use it)

ext4 filesystems cannot be read under current drivers, if extents option is enabled ( and I believe most distros using ext4 do have extents enabled by default).

keep the home folder in ubuntu where it is, but create symlinks for the Documents, Music, etc folders to an NTFS formatted Data (A2) partition

This is my current setting as well.