Well, I guess I would do the following. (Kinda what Rx suggested earlier)
1. Create file on computer..name it "sd card"...or whatever.
2. Download rom zip and place in that folder.
3. Make nandroid backup on phone.
4. connect phone to computer and transfer nandroid to the "sd card" folder.
5. Transfer anything else currently on sd card you would like to save (photos etc)
6. Disconnect phone from computer.
7. Boot into recovery.
I dont know about Clockwork recovery, I can only base the following off of Amon ra.
8. Once in recovery, format card and partition if desired (I recommend it) See link ocn provided and scroll down and you will find instructions on how to partition.
8a...Stay in recovery..
9. Plug phone into computer and find option in recovery to mount usb/ms toggle.
10. Transfer contents of "sd card" folder from computer to phone. Then unmount.
11. Still in recovery, wipe all except sd card (since you already formatted it and have
only items from "sd card" folder from computer on it.)
12. Wipe everything except sd card again. I usually wipe 3x.
13. Flash rom.
14. Your recovery and bootloader ain't going anywhere, dont worry.
15. Sign into gmail after rom has settled in and contacts/calendar/mail should sync up.
16. You now have fresh rom install, with minimal stuff on sd card.
Again, I dont know much about Clockwork other than it can be buggy and was suggested to flash Amon Ra recovery....it's much more stable/problem free. Depending if you are s-on or s-off, I believe there are different PC36IMG files used to install it. (Also in ocn's link)
When you wipe everything except sd card, it wipes your phone clean. As if your phone was new.
This is kinda like if you bought a new sd card and wanted to use it.
What size/class is your current card? I recommend at least 16GB, class 6 or higher.
I re-read my procedure and I think this should work. I would feel comfortable if others would concur.