Very Nice pics!! How about some of the finished product?
The stock kit was made to fit the stock battery boxes......
The stock electronics will fit without the shim as long as the proper number of spacers are used in the rear motor pod attachment. The kit essentially lowers the ride height between .5+1mm. If you are using stacked FET's then you should trim the chassis to clear the FET's.
The X Plus kit is better suited to aftermarket electronics and all sorts of battery configurations. With the flat pan it is ready to hack to fit the batteries of your choice...............