Not Cool!

You may be onto something with the trans cooling loop, but I've never heard of that being a problem. If the viscous clutch is bad, that is probably your problem.
Where is your fan shroud???
They really do work. The auto manufacturer's of the world would not use them if they were not necessary.

P.S. Have you thought about using an electric fan?
I installed a 16" with a shroud hooked to a thermostatic switch and a relay. That car never ran so consistent with the belt driven fan.