Hi Alkay, I quickly read through your posts, the colour and paint is entirely up to you. Sure I think a red or brown stain on that cap would look great. If you don't like the look of that you can always sand it off and paint solid.
At this stage don't worry about a shim. You should have enough adjustment in the bridge height and truss rod to set up the string action and playability.
These kits the neck is supposed to be on about a 2 degree rake angle toward the back of the guitar so don't play with shims at this stage. This is to compensate for the higher tune o matic bridges