Your manometer should have a useful control output to 2.5 decades below full scale but you can push this to 3 decades. You are at the hairy edge. The real issue is how much output you have (0.5 microns is 50 mV from the manometer) vs your gauge's resolution and how much noise you have in the system from your hv supply, etc. Make sure you use factory cables and shielded connectors (100 mT manometers should have D connectors as standard).
On the throttle valve, the question is whether the valve's conductance characteristic is adequate for the pressure range and gas flow you are operating at. The valve you have is provided with a range of diameters so I can't tell from your note what you have. Check the MKS Web site (www.mksinst.com) for specs and don't hesitate to call one of their valve apps engineers. Usually at such low pressures you'd control with an upstream solenoid or piezo valve.
Steve
Created on Friday, April 13, 2001 2:43 AM EDT by Steve Hansen