The IDE cable that you use CAN determine the drive letter of the HD. My computer, with the dos from this site, usually detects the HD no matter where I put it.

Which cable you use can also determine speed. If the laptop HD is the only drive on the IDE cable, the transfer speed will be noticeably faster. (Ideal )

I am saying this from my own experience. The above is not law! What I am trying to say is that I have never run into a problem with switching ide cables, although it might happen.

Now about your problem, make sure that if you are copying in windows that you are NOT compressing them. Dos cannot "see" any files that are compressed by windows. Can you see the files in windows after you copy them? Do you get an error message?

I you are using dos, mistakes are easily made. I recommend using the "explorer" add-in, and visually coping the files from the left and right drives.
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Also, I wanted to point something out. I'm not meaning to criticize the tutorial that you are following in any way, but formatting a drive fat32 and converting it to ntfs after you install windows, can be a HUGE mistake. You see, windows doesn't like anything moving the system folders, and that is what happens when you convert a drive to ntfs.

I HIGHLY recommend making two partitions, one fat32 (for dos) and one ntfs (for widows). Make sure that they are both logical drives and that the fat32 partition is the primary. install dos, and continue as the tutorial describes.

This is very tricky. You must really know what you are doing. I just did this whole thing a few days ago. If you need step-by-step instructions, just ask. But trust me, all of this trouble is worth it in the long run.