I ditched the 5D today and took (once again) to the Epson scanner. I've done this sort of thing before, but there is an article in this week's Amateur Photographer on scanning flowers which uses a slightly different technique. You need a scanner that scans film strips/slides. You place the flower in the slide strip and the exposure light above is just wide enough to scan a small flower. In the dialogue for the scanner you set document type to 'film', and film type to 'positive', with 48bit colour and resolution of 1200. On my scanner you can do a preview, then select a marque tool which allows you to just select the flower area to scan (rather than the whole strip). Then you scan it. In PS you invert the image to get a negative and then play around with the channel mixer to get different colours.
Needs further refinement, I think, but interesting. C&C along the lines of 'Rob has finally lost it' sort of welcome...