Well after giving this much more thought, I have decided to make my own wheel bays.

The plan...
Soak some balsa and rubber band them around a paint can
Make templates out of poster board to know where I need clearances
Tranfer templates to balsa and cut them out
Glue them in and finish with some Zinc Chromate colered paint and call it good.

I think this will look a little bit more "scale" than the wheel cups that were included in the kit, plus I can but a bigger wheel in - 3".

What do you think?