Final update:
Car is finally back together I ended up reusing the locknuts for the drive shaft with a little blue locktite on the threads. The exhaust system is a bear to install in one piece. Car drives well and the whining and ticking sounds that bothered me at highway speeds are gone now. I used Permatex Thread Sealant on the transmission flange nut and I'm wondering if I should have let it sit for longer. It indicates that it cures in 4 hours. I drove the car more than 4 hours after application of the sealant. I guess I'll just have to be on the look out for a leak. The car idles much better with the new oxygen sensor. Engine vibration is less pronounced inside with the new motor and transmission mounts as well. It seems as if now during acceleration the engine drone is more pronounced. I know the exhaust pipes are installed properly and torqued to the exhaust manifolds so I'm ruling out a leak there. The exhaust and transmission are now mounted with new stiffer rubbers, so perhaps they simply transmit more noise and vibration from these components into the cabin? All opinions and advice are welcome