yes you are correct, it would be best if it was tweak free before mounting the top plate on. I've just finished the build and will have a run the next few days. Until then and beyond, I will look into a type of system to keep it tweak free, just your post doesn't completely make sense to me as I have only just completed building the car and don't know the ins and outs yet.
I also have a feeling I need to do some dremelling as at the moment putting the spur assembly through the bulkheads requires a little force to get it in, and I'm also thinking this is contributing to the tweak.
I don't understand why they didn't design the 'motor mount brace' to mount completely flush with the chassis.