I bought a new chrome alternator cover from Summit. The mounting ears are off by 90 degrees, for my 69. Is there a trick to rotating the covers 90 degrees w/out fouling up something on the inside?

You should be able to unscrew the four long bolts and turn the rear housing along with the liminations of the stator windings and turn it with respect to the front housing to where needed.

Remove pulley, remove 4 bolts, place alt on bench with the shaft facing up. Lift front cover without lifting rotor. Move to desired location and install 4 bolts, them pulley.