I added 1.75" long 5/16-24 Screws, Washers, and Nuts to the Agilent TwisTorr 74 Turbo Vacuum Pump to a CF 4.5" Flange to KF 50 adaptor. Neither flange nuts nor washers fit next to the turbo pump, so I just used regular nuts. We still need to tighten the screws. 1.75" long screws were the perfect length for this application (matching the length of the nuts), but 2" screws, which are standard for connecting 4.5" CF Flanges with through holes, would also work.
I tightened the bolts to 34 Nm (incrementing by 3 Nm from 13 Nm) with a 1/2 open faced wrench holding the nuts. Tightening the bolts without the wrench did not actually compress the copper gasket. The gasket was still a bit visable, but it will be easy to tighten further if needed.
It looks like the manual recommends 20 Nm: https://www.agilent.com/cs/library/usermanuals/public/TwisTorr%2074%20FS.pdf