There is no way using the wrong firing order did any damage to the camshaft. As long as the engine fired up and ran at around 2-3k rpm for 15-20 minutes during break-in, it will be fine. The reason cams need broken in like this, is because the lobes are lubricated by the oil that gets slung off the crank. There's not enough oil at idle passing through the system for proper break-in (especially with strong springs).
It doesn't matter if the engine was running on two cylinders... as long as it was up to speed, you're fine. Even if you had to crank it for a bit before it fired, as long as the cam/lifters were greased up well, they should be fine.
289/302 cams work just fine in 351W's... as long as you change the firing order. They don't run any better... or worse.