Time for a thread revival.
It turns out I was incorrect thinking the issue was exhaust related. The trans died right before Christmas and has been replaced with a lower mileage (140k) unit out of a lx450. Shifting is improved and the noise is GONE. In retrospect I should have forked out the cash to have a transmission specialist diagnose the old unit. I am leaning toward an issue somewhere in the valve body, likely an internal seal based on MUD suggestions. It did get down to -20 the night before it finally died, so I wonder if the cold temps helped a failing seal to finally die.
Final issue was excessive shuddering at speed, slippage, delayed gear engagement, and finally no movement in any gear. The unit went from functioning to dead in under 5 miles.
For anyone curious here is the cost breakdown of the swap. I wish I had this info available when I was considering options. It seems like some people here do not want to disclose how much they spend on their trucks, but I think having that info around is helpful to the community.
Used Transmission from Yota Yard in Denver. $500 and $50 core charge
Labor for the swap - $942 (@ $105 and hr)
Fluid, new trans seals (input & output) and a new rear main - $212
I had them hold off on cleaning / replacing the filter since that is something I can do in the driveway.
Overall cost - $1652
I will be keeping the old transmission and will tear into it in the summer once my work space is warm. If the issue is discovered I will post back here with an update.