The accuracy of a clock depends only on the length of the pendulum, and if you're interested not the bob weight either. A light bob can give the same accuracy as a heavy one provided neither is under the influence of "drafts" from doors or furnaces etc.
You can scale the gears to any size you wish but I would keep in mind that our ability to be precise is somewhat fixed and a 0.001" deviation is probably as good as we'll ever get in wood. That deviation in a 0.5" pinion is on heck of a lot more critical that the same 0.001" deviation in a 2" pinion.
I will go for the largest gear size that is practical for my application and prefer gears that are in the 8" or less size and that limitation is because my WidgetMaster Midi CNC can only cut an 8.5" item.
When scaling I agree that if you have both the gear and the pinion on the scanner at the same time you'll have a lot less chance of getting different scales. Another thing that I do is to put a 6" circle on a clear plastic overhead and put that on the scanner first then when I scan and go to a program it is easy to tell if I have some distortion or not. I also use this idea when printing if a part needs to be cut on a scroll saw or band saw. Printed copies are nearly always distorted. I correct for distortion in Powerpoint where I can change either the width or the lenght to come back to "round".
If you get to the point where you want to do more on your own designs there are some good computer programs that will produce "perfect" tooth forms in either cycloid or involute design. I always go for involute myself.
John