line up if piston #1 is at TDC of the compression stroke or be near if the crank sprocket moved or belt not on correctly even though the teeth count is correct. 2 revs of the crankshaft is 1 rev of all the cam gears so every other rev of the crank the crank timing mark it will come to TDC of #1 piston, basic to all 4 cycle Otto engine operation. Verify this simple test B4 going doing major removals.
Yes if you sheared the key the crank sprocket will slip on the shaft. Bitch to remove if you cant get the nut so heat the nut with heat and try. If that doesn't work carefully split the nut with a cold chisel and try not to damage the threads on the crank.