You may want to rename your CDROM/DVDROM drive to E instead, so your data partition will be called D: instead. Its a bit more tidy.
Don't mess with boot flags and stuff; leave your system drive as is. If you want to save your user files on the D partition, set your program location to save to D partition instead.
For example, you can configure Firefox to save all downloads in D:\Downloads instead, and create D:\Movies D:\Pictures etc. Whatever you want.