Not sure about the spacers, I found it was tight when new but quickly wore in and then became loose, maybe shim it after a few days of running when things have bedded in well.
Yes I did quite a bit of dremelling so that the batteries would sit down flush with the bottom of the chassis. No going back with the chassis!!
I would recommend starting with the stock setup...as you said.....
I like running it best with the one-way pulley locked up and a front one-way diff installed. I use the HPI Pro2 one with the one-way bearings reversed in their housing. I think an X-ray one should fit, but I don't want to use any X-ray parts on my car!