Making a custom chassis...need some advice on placement of the center diff.

[What's_nitro?]

So the battery tray is installed? You could take the CD/Motor assembly and set it on the chassis (without the CVDs) and move it around until the balance is right. If the battery is centered F/R then the motor will have to be farther forward to even it out. Custom CVDs may be in order if you want it "just right".