Jon,
I had to drill 5/8" holes in my 1" frame rails and use ferrules like you have made for the lower motor mount and it's a PITA. But it's not too difficult to start by using a small center drill first, then using a step drill. This works well if you can fit your drill within your frame rails. I, like you, couldn't. So as I opened up the outside with the step drill, I progressively (to try to preserve alignment) increased the twist drill size as to the same size as each step on the step drill. When I got it big enough for a 3/8" drill, I welded a piece of drill rod onto a standard 3/8"twist drill that was long enough to go thru one side, thru the lower motor mounting lug on the base of the motor, and reach the far side to ensure alignment. Ideally, you should try to find a right angle drill to drill from the inside. Those big twist drills simply do not like to drill thru tubing without catching and trying to break your wrist.
Now I just noticed that you have figured out a way to do this, but I'll post this anyway for anyone else who may have to do the same.
Tom