Did you cut back 1/4 inch off the spark plug wires and test again? I double checked the manual and it is supposed to be 9 - 15K. You mentioned you used another MPEM from a good working machine, can you also try swapping the ignition coil?
You do not need to retime the engine if you only remove the flywheel and put it back correctly, timing would only change if you adjusted the position of the stator behind the flywheel by moving it clockwise or counterclockwise, but in order to do that you would need to remove some bolts so you will be fine. To remove the flywheel, you will need to remove the nut and a puller to remove the flywheel off the crank, if you don't need a puller then your woodruff key is definitely sheared. But first try removing the nut and looking down the little slot to see if you can see the woodruff key sticking up, I have done this all before without removing the engine and have used my phone with flash to take a video to see the key is in good condition after removing the nut.
You can test the stator to check the generating coil and the battery charging coil.
generating coil: resistance between black and black/red wire from the stator should be 40 - 76 ohms
battery charging coil: resistance between yellow and yellow/black wire from the stator should be 0.05 - 0.6 ohms.