You can always test to place Skyrim game files at the beginning of the disk and see if the stuttering has gone.
The bad thing on the standard data disk monthly sript is that it sorts the whole disk with "sort by name" and Skyrim folder will therefore be placed quite end of the disk. If you don't want to make a new script just add new zones for Skyrim and Deus Ex or your "games" directory before the last zone 3 on daily,weekly,monthly data disk sripts.
example of Zone for Skyrim that sorts files by their size (see other possible File actions
/* Zone : Skyrim */
(LastAccessEnabled(yes) and LastAccess(,1 month ago))
# Sort the items from smallest to largest.
If you don't see any difference then maybe your graphic card's vram is too small or system ram, and the game needs to swap files between pagefile and ram/vram when loading new textures? But I don't believe you have "slow" gpu as you get decent 50-60 fps.
This post from BloodySword sums pretty well the best drive layout for systems with games and the problem with pagefile:http://www.mydefrag.com/forum/index.php?topic=3666.msg21981#msg21981
... The cause is, while gaming, huge paging will occur. The drive must move its heads to the pagefile.sys and then to the game ressource files. Therefore it is much slower, even if you have much RAM. Today's games are not optimized for 64 bit. So the limit of physical memory is 2GB per process (working set) and the game won't get more than that. Paging WILL occur, even on a 64 bit system.