It's most peculiar... the reason why the vacuum pump was locking up was that I tried to use an O-ring that was 0.7mm thicker than the original. The new alternator shaft was the perfect size.
First, I went with Philip's suggestion and tried to flip the rotor... however, in my vacuum pump, one cannot put the rotor in the wrong direction. One side of the rotor is machined out (about 2 quarter coins deep) and the back cover has a corresponding circular protrusion. So if one tried to put the rotor in the wrong direction, the back cover would not be able to go back on, it would stay 2-3mm ajar.
This picture shows the old O-ring on the left and the new one I tried to use on the right. As you can see the new one is almost a perfect match as ID is concerned.
Here you can see how the new O-ring fits the groove on the vacuum pump (I am still hoping that some one recognizes what kind of vacuum pump I have).
However, when one looks at the side profile, the old O-ring is much flatter than the new one (1.72mm vs 2.54mm).
I didn't want to believe, that such a small size difference would make the pump lock up, so I switched back and forth b/w the 2 O-rings twice to ascertain that THAT was the problem... But no doubt. I guess what might have happened was that when I bolted on the vacuum pump with the new O-ring, the uneven clamping force (the bolts are not 120 degrees apart, they are distributed somewhat unevenly around the circle) must have caused the housing warp a tiny bit, which led to the lock-up.
A valuable lesson learnt: "One should not screw with O-rings, because they will screw you back !!"