I was holding them in a modified collet. Thanks for all the advice everyone on here has given one. Once again I though the answer was simple but it will keep me busy for 6 months.

How are you holding the screw for polishing? Typically it would be held in a tripod tool if going for a flat polish. I would recommend a couple of paper steps before polishing, I typically use 20 micron for serious flattening then 12 micron and go straight from there (after cleaning) to diamond paste, Aluminum is not a good substrate for polishing, the surface oxidizes in minutes and that is as hard as ruby. If you don't want to find or make a tin or zinc plate, thick plexiglass works well. Roughen the surface with a clean file before using.

polishing or restoring screw heads is an art !       with a lathe (or a drill press)  cut the head and then go to "wet and dry" sand paper to 1,000 grit,   you are done.  the slots are a whole different art.     vin  

The original application to build the "UK Time Corporation" factory that became Timex Dundee was posted by Timex in January 1946, according to this article. https://www.eveningtelegraph.co.uk/2016/01/29/dundees-timex-new-group-to-archive-stories-of-controversial-factory/ Production began in the early fifties and Timex produced watches and a variety of other hi-tec products there for 47 years. Little remains of the factory complex now, most of that area of Dundee having been "redeveloped" into the usual collection of out of town shopping centers and small industrial units.

Doubt that diamond paste will be effective on a filed surface as it will be 'rough' by polished standards.  ! would start with wet&dry papers going down to 2500 grit then go onto the polishing pastes.  Thoroughly clean after every grit/paste size and do on a flat plate.  Dialux bar polishing medium (grey I think for steel) may be better than diamond paste.