Alvin,
I have used the exact same device and procedure you mention and it worked well. I loosened all the main bearing caps but never thought about the transmission.
I think I actually pried the crank down a bit to gain a little extra room. I do remember slopping STP all over the rope as I pulled it through. Patience and plenty of slick-um is the key to getting the upper half in.
I don't think I would attempt this with any tool other than the finger trap that totally encircles the rope..they will not slip off by pulling too hard!
Stuart