Okay, first of all, even though you know it, I have to cover my butt by saying BACKUP EVERYTHING FIRST. ::ahem::
Now that that's out of the way...
Assuming that drives C and D are on the same hard drive and are on the first IDE controller (most likely labeled in white micro-text "IDE 0" on your motherboard), then what Windows sees as drive C: is going to be /dev/hda1. That's Device: Hard Drive A (the first), partition number 1. Drive D: is, then, /dev/hda2 (Device: Hard Drive A (still the first hard drive, speaking of the physical unit here), partition number 2). If your data is on drive D:, then it's on partition /dev/hda2.
So! All you have to do is BACKUP
your My Documents folder and set up Linux install. Depending on your distribution of choice and mode of formatting, your actual steps to do this will vary, but what you'll have to do is format /dev/hda1 as a Linux partition and install Linux onto that.
As to migrating your data from your Linux partition to the soon-to-be-formerly Windows partition, I wouldn't even go there. Recommended course of action is to back up all Linux stuff you can't live without (everything under /home and all the .conf files you've maybe tweaked by hand) and do a fresh install. I would point you to a site on hard disk cloning over through netcat and dd through an existing Linux machine, but that's Expert Level stuff and a pain in the arse besides. If you decide to format and do a fresh install, of course, you COULD just leave that existing Linux partition intact and keep that hard drive in your machine, and migrate the data piece-by-piece from that HDD to your new partition.
In other words, you could mount that second hard drive (if it's the slave drive on the same IDE controller as your main hard drive, it's /dev/hdbX, where X is the partition number in which your Linux system resides) as a folder on your new system and copy /home and such things over yourself. I've done it, it works, it's fairly safe; the only major drawback is that if you haven't prepared your Linux system to be backed up and restored easily (by hand), then it's a pain to deal with remembering all the files you need to move.