I can't imagine why you'd have any washers between the motor mount and block. One between the block and the nut is all I can think of. Lowering the engine down will help out your roll center. Not a huge amount, but every little bit helps. I guess it depends on the setup of your engine and motor mount.
For the positioning, it depends on how long your chain is, how much play you like in your chain and only the very slightest bit to do with the scales. If you use the same length chain all the time and increase the rear gear, you'll end up moving the engine back by default (to keep your chain play). You don't want too long of a chain, you don't want too short of a chain...so the positioning doesn't really matter as it will be adjusted with gearing changes IMO.