The shorted pins are 1&2 (they count counter-clockwise from the notch) and are both GND, so nothing to worry about apart from cosmetics.
I was talking about the ROM tower orientation: the connector to the mainboard is soldered to the tower's PCB. One pin (pin 1) should have a square solder point (or differing some other way from the rest) - this one is to be oriented towards the side where the mainboard socket's notch is.
In addition, the two ROMs 'hanging' on the ROM tower also have notches or a blank spot indicating pin 1 (as might the socket used for gaining height). Everything I've ever seen shows the tower goes to the two topmost sockets (U182/183).
And yes, the tower ROMs do seem to differ from the ones that go directly to the mainboard. I can't confirm this from my own experience, but I've heard it several times. Apparently you can't use 'mainboard' ROMs on mainboard revs that use a ROM tower.
