Having followed previous and past posts on these topics these are my set-ups,
a) cutting;- I use a cheap builders tile cutter with a diamond blade (the continuous diamond compound rim). the scribe method leaves nasty edges. When used correctly with the built-in water cooling there is no glass fiber dust. tip;- add a few drops of washing-up liquid to reduce the noise.
b) drilling;- having dismal results with the dremel drill and stand I've changed to proxxon drill, stand and compound table (This screws to the stand and has scroll wheels that allows for precision setting in both X and Y axes. gone are the "wandering" bits, snapping of bits non-existent, with near perfect centering of holes. TO THE ADVISORS......BIG THANKS!!!
c) artwork preparation;- on completion of my board layout, I place a copy on the desktop, rename it to xxx final (xxx = your file name) and open. change all of the pads to a 0.5mm hole size before printing. this steps further reduces the "wandering" problem and eliminates the center punch. This step really helps with registration using the "5 holes outside the board outline"method. Most PCB programs allow you to adjust the same type pad size properties on a global scale.
Hope these notes are of some use, and wish you all the best on your current project,
chester