Since you are going to be checking your backlash with the housing put together here is how I would do it. I would put a bolt in one of the stub axle holes that the wheel bolts to. That should be the appx diameter of the front drive gear. With your indicator fastened to housing with magnet base, c-clamp or whatever, then put the point of the indicator against the installed bolt. You can then measure the movement back and forth while feeling the gear contact. You need to be measuring at a distance close to the diameter of the front drive gear. Anything further will give a larger reading, anything closer will give a smaller reading. Hope this makes some sense to you.
Do you not recommend checking backlash with the housing off? (it is currently assembled with the housing off)