These things may have helped slightly but did not fix, found from other threads with the same problem -
1) Opened D3Prefs.txt and changed HardwareClass "1" and DisableTrilinearFiltering "1"
2) Run in Compatibility Mode Windows XP Pack 3 and as Administrator
3) Task Manager, Show all Processes, right Click Diablo3.exe - Set Affinity....Turn OFF Core 0
4) Task Manager, Show all Processes, right Click Diablo3.exe - Set Priority High or Realtime
5) Freshly Reinstalled Graphics Drivers
6) Turn on/off indexing on my SSD Hard Drive
7) Changed and tried numerous settings in game / Nvidia Control Panel Settings
8) Performed various Windows 7 tweaks on my hard drive settings
9) Created a RAM drive and put some of the game files on it
10) Ran the game files from USB stick
Some of the above helped, but did not fix the micro stuttering.
I KNEW it was caused by access of game files and hard drive access.
No matter how many tweaks i tried, i could not ELIMINATE the stuttering until............................................
11) I simply turned off real time protection on my anti virus software. (microsoft security essentials).
Basically whenever the SDD was being accessed, real time protection was scanning them for viruses etc, and thus the game files were being accessed multiple times whilst they were trying to load in game.
Such a simple fix. Game is now 100% smooth with no stuttering at all.
Hope this helps some people, who like me, tried everything but the obvious.