No need to switch out the differential. The Yokomo differential is great, sand the differential rings, throw in ceramic balls, add 2 extra bevel washers and your going to have a uber differential. Don't muck around with the Tamiya differential.
The 0.4 spur gear is Tamiya's own pitch. I would stick with the Yokomo spur gear and just work with that.
The F103 tires and rims will work. I have them currently on my YRF.
The YRF is an awesome machine, I'm very happy with it.
I would suggest working with the kit setup first. Really, really pay attention to the instructions and if you put the time and effort into the build it will pay off.
Preparation is key to a good handling r/c .