As was mentioned previously, the change in the shift pattern may just be the transmission using a different set of shift-points until it is warmed up.
Hopefully someone with this (NAG1) transmission can confirm - but I know an altered shift pattern on the 545rfe is normal in cold weather.
As for the "shaking" at stop, what are the RPMs at that time? It could simply be that the idle speed is too low for one reason or another.
Of course...it could also be the ground trembling under all that torque the diesel puts out