Both of the 2/3 valves control the EGR. If I recall, the upper valve closes the EGR at full throttle and the lower valve closes the EGR at idle (I may have those backwards). The EGR is supposed to be open at all other times once the engine is warmed up. The only way that the valves affect the transmission is if they leak, which reduces the vacuum signal to the modulator and causes clunking. If your EGR is disconnected, then these valves serve no purpose but to dump vacuum. You really don't need them. Try disconnecting the two lines that go to the 2/3 valves at their source, and I'll bet that you see a significant increase in vacuum being sent to the transmission. I'll bet that the clunks disappear, too! Not only that, but you won't have the EGR valve blowing soot into the engine.

__________________
1982 300D, black w/ palomino leather, 203K
2001 E320, champagne, 105K (Mom's)
1999 Dodge Dakota, squeaky & battered, 142K