The base valve is the one that you pull the first 2 shims out of. The shims on the damper rod are for rebound I believe. I weigh 180lbs and pulled two shims out, used xr .43kg/mm springs with 20mm preload, 7.5wt oil 120mm from the top, clickers 16 out. I can soak up the square edge stuff great, and even do some light mx with the bike. If I get more that 5 feet of air and don't slope the landing it will bottom, but not that hard.
Let me clarify, the XR springs were aftermarket replacements from Eibach that measured 512mm brand new 996 series IIRC.