Tightened all of the vacuum ports on the chamber so that the flange interfaces are all now metal-to-metal, ie full copper gasket compression. All of the ports required at least two star pattern passes before reaching this point, except for the bellows line to the turbo/backing pumps which was already at complete compression. Prior to tighening, the wide range gauge gave a pressure reading of 5.8x10^-6 Torr and the ion-gauge showed 5.75x10^-6 Torr. After tightening the wide range flange the reading dropped to 5.6x10^-6 ; after tightening the ion-gauge flange the gauge reading dropped to 5.69x10^-6. 

For future reference: the 4.625" flanges use 5/16" torx bolts and 1/2" nuts, and the 2.75" flanges use a 1/4" torx bolt and 7/16" nuts.