Is the misfiring only during start up and runs fine thereafter? If it misfires throughout do the following:
First you need to identify which cylinder is misfiring or not firing. You can do this by doing the "plug wire pull" to see if there is any change in the engine tune or if the engine dies. From there, switch the coils (always mark which one is which, it is very easy to lose track which one belongs to what cylinder) and see if the problem follows. If problem follows then you know the coil is bad. You might want to do this with the old coil you removed. And if you confirm the same coil is bad then you probably had a bad new coil.
If the problem does not follow, then you know both coils are good. Now it is time to escalate the switching of parts. Unfortunately, with only two cylinders there is only one CD module hence you cannot switch it around unless you have a spare one that is known to be working. However, even with one CDM, each CDM has two ckts in it with respective inputs and outputs. A wiring diagram will be very helpful. You can switch output wires from #1 (orange or blue/orange) to those of #2 (red or blue/red) at the same time you also need to switch the input wire from the trigger (white grn or white and white red or red) to the other input wires (white orange or green and white yellow or orange). Again check to see if the problem follows.
If it follows then one of the CDM ckts is bad and the entire CDM needs to be replaced. If it did not follow, then problem is most likely with the trigger. You need to do cold resistance check with the trigger first to see if there is any discrepancy based from the service manual. If there is then you might want to investigate further. If there's none, then it is time to check from the mechanical side i.e. compression, reed and carburetion. If you have a compression gauge you might want to do this initially to get it out of the way. Or if you are more mechanical incline rather than electrically, then start with the mechanical first.
I'm not sure what year is your 50HP but the above diagnosis is based on the 1988 "D" and later model.