Alright, now that I am mostly confident I did this right, here is what I did. Please, if you see anything that requires a comment or can be done a different way, share.
I prefer pictures when reading a shop manual as I am not always familiar with the names of parts. This is meant as a supplement to the actual manual. My Ninja is a 2012, yours may not be as pictured.
Please forgive the overall condition of my bike - she’s had a tough life.
First steps are to remove the alternator cover.
Note: the shop had already unplugged the stator up near the air box so unfortunately can’t advise on that.
Remove the lower fairing:
Drain the oil:
Drain the coolant:
Remove the shift lever from the shift shaft
Remove the engine sprocket cover
Remove the two water pipes - this took me a second to figure out. The clamps on the top are easy enough, the lower part of the pipe slides into the water pump. Firm twisting while pulling got the pipe out as the o-ring inside sealed it really well.
Remove the alternator cover. I removed the bolts in sequence and kept them in order as they are different lengths. Removing it involved being firm as it is magnetized and seemingly stuck on there. When it eventually popped loose, my hand bumped the starter idle gear inside and knocked it off onto my table. Talk about a panic moment! You will need something to rest the cover on as the cord going up to the plug will prevent it from resting on the ground.
And now you can see why I was removing my stator. Kinda crispy!
The gasket around the cover may be stuck on the cover or to the engine. Either way, this will need to be replaced.
Now the delicate work!
Remove the screws and clamp over the crankshaft sensor
Remove the lead grommets - these are rather stuck in the cutout of the cover. The original sealant is a sticky black goo that holds them in well.
As noted above, the plug on the 2011(?)/2012 is really large and I had trouble removing it. In the end, I followed the de pinning suggestion and that worked wonderfully. I tied a string to the end and let the wire pull the string down as I pulled it out from the bottom. This allowed me to tie the new one on the end of the string and feed it back up the original path.
Depin the new stator - here is some clear pictures of the process.
Feed the new cord up and replace the plug.
Now just reverse the process, starting with putting the lead grommets, crankshaft sensor, clamp, and screws back in place. There is a rubber bumper type thing that goes between the stator cord and the sensor. The Electrosport stator I bought had a really stiff cord, so this part was a challenge.
Replace the stator bolts - use the manual to learn what torque.
Then you replace the gasket. Unfortunately I didn’t get in progress pictures of this. What I did was cleaned the cover and front of the engine as much as I could to get the old sealant off. Then I used a very thin coating on the rim of the cover and gasket, then placed those two together. I then put another thin layer of sealant on the outside of the gasket and the rim of the engine and slid the cover in place, holding it there for awhile to ensure a good bond.
Replace the water pipes
Replace the engine sprocket cover
Replace the shift lever - unless you remember exactly how you had this, may want to keep the screw loose so it can be adjusted.
Plug the stator back in. Bad picture, I took it before I plugged it back in as I was happy I had the bike back together!
Replace the oil and coolant.
At this point I started the engine up to make sure I hadn’t broken anything. FOR ME my battery was unfortunately dead, which led to problems that were thankfully resolved by spending a night on the tender.
When I first started the engine. I noticed I was leaking coolant from the upper of the two pipes. Turned out I had overtorqued the bolt. When I loosened it just a bit the leak stopped and it hasn’t leaked since.
I ran the bike a few times in the garage to make sure it started and that the battery remained charged. Then this weekend I took the bike it for a short 15 ride, then 30 minute ride, then 2 hour ride. No issues cropped up so I’m hopeful that everything now works as it is supposed to.