So I think I undesrtand what the problem was. I was following this guide:
for mounting and then reinstalling Grub2. But since I had made a seperate /boot partition, I should have followed their instructions carefully on mounting /boot...and I didn't. I just did it the normal way, mounting the sda5 partition. In any case, I found that out too late, and instead deleted my ubuntu partitions and did the Ubuntu install again, this time following the install instructions on this page : http://www.ubuntu.com/download/ubuntu/download
instead of trying to create my own partitions manually.
Worked just fine, and now grub, windows, and ubuntu all work well and as expected.
thanks for the help!