OK... Since nobody else has posted this, I will...
The reason that your SD shows up as 40M (no matter what its physical size) after going through the nooter rooting process is:
The .img file that you dd to your SD card writes not only the data on the SD card but also the partition table. The partition in the nooter .img file is ~40M in size. The Nook Color doesn't look at the physical device but rather the partitions on the device. Since the partition is ~40M, that's what shows up.
/me is praying for the day that people RUN SCREAMING away from Microsoft operating systems.
Just FYI... Android == Linux. Embrace your inner n3rd.