As I said, for very good reasons, I have three drives fitted,
C: drive - 400 GB unit, 84 GB used (always used – main drive)
D: drive - 300 GB unit. 19.5 GB used (always used)
E: drive – 200 GB unit. 105 GB used.(used occasionally – for storage of documents, images, pdfs)
You say that these are used for very good reason, what if the E drive failed, if that is the only drive being used for backing up docs and the amount of space unused, just use the one disk (400GB)
a delay like the one you have described can be down to years of installing/uninstalling programs have a look in msconfig then startup