My HDD (SATAII) has three partitions, C, E, F with the Optical drive as D.
Now when I got the system it was a single partition C I try to keep my data separate from the windows partition, a) it makes back-up easier up to a point, b) if you have a problem with the C partition you can restore just that partition (drive imaging software). I keep data back-ups, partition image back-ups on the 3rd partition and also back those up to an external HDD, in case of an internal drive failure.
The problem with the drive order is I believe the mix of SATA and IDE with the IDE taking the second drive letter, rather than all partitions in the SATA drive being in order with the IDE optical drive taking the next drive letter.
Yes I believe it is possible to re order the drive lettering (I believe I got similar errors or the re-lettering didn't stick), but I didn't spend much time trying to resolve it, I just got used to it.