The post '61 390 blocks have an alternator mounting hole in the front as well as the holes in the side for mounting the original generator bracket.
Early 390's prior to '63 did not have the coolant running through the carburetor base plate. It's possible they reused the 352 manifold.
All Thunderbird COM's beginning in 1961 had the vacuum modulator.
The 1964 390 motor mounts are identical to the 352 mounts. You can reuse your original trans mount on the 1964 COM.