Installing Windows after ubuntu on a separate HDD?

Installing Windows will overwrite the MBR anyway (had this problem some time ago). The way you can get it working, is to physically UNPLUG the drive with your Ubuntu, by completely removing it from your computer, then installing Windows on the other drive, and re-plugging the drive with Ubuntu.

This way you will be completely sure MBR will be okay, for Windows installer will have absolutely no access to the drive with Ubuntu, as it will be separated from your computer (but some people advice it is even safer too temporarily keep the unmounted drive in a separate room, just in case [not really, I'm just kidding]).

This way you will get both systems installed on separate drives. After re-plugging make sure to alter your BIOS setting - you want to start the boot from the Ubuntu drive, as that's where GRUB is. Note that on first boot you will (most probably) not have an option to boot Windows. To fix that, boot into your Ubuntu and run sudo update-grub, this should detect Windows and add it's entry to the boot menu.

Windows likes to be the big I am & will believe itself to be the primary OS. This can cause problems, for instance, when effecting a repair install (therefore wiping GRUB.) It is best practise to have 7 on primary disk (sda) & Linux on secondary (sdb.)

You can then alter boot order in BIOS, or if this is not possible, use EasyBCD from within Windows. Since you have separate physical disks you have some redundancy if one should fail. Might be a good idea to keep an image of 7 on NTFS partition on your secondary Linux HDD. & also image just your Linux partitions with Clonezilla to your primary Win HDD (no point having an image of an image!)

Hope this makes sense...