I would put it back the way you found it, as that is most likely how it was all along.

If anyone changed a coil over the years, they most likely put it back the same. Otherwise, I think you're over-thinking this vibration thing. It's getting hammered no matter which end the lugs were mounted. Properly soldered wires and diodes should not be breaking loose in either case. EDIT: As others have stated, you may also create new issues with wire lengths and mechanical clearances.

For things like slings the lugs are normally on the coil stop end. Otherwise the lugs would be mounted low near the playfield. Might find this causes clearance issues with the linkages, lamps, wiring etc.

I think you're going to find that you can't swap the coils around on most of them due to how the wires are in the harnesses. You'll also have to think about locations of other metal brackets and assemblies being too close to the lugs. The only coils I keep the lugs away from the stops is flipper coils.

If I come across a machine with the diodes on the coils, I make sure they’re up when the playfield is up in a machine when putting back in.