UPDATE:
After hours of work, and getting my hands greased up and washed several times, I finally got the coil boots out of the sockets. I replaced both ignition coils, and the check engine light is off, and the car runs great.
To access the coils, I had to remove the air filter, engiine cover, and unclip several other parts. Then I used WD 40 to loosen the rubber. I drove around to warm it up too.
Then, using a flashlight to look into the ignition coil chamber, I used a long pick tool to go around the boot and loosen it up. Finally after much tugging and more maneuvering with the tool, I was able to remove the boots. I can't tell you how satifsying it was to remove them.
Although the outuside housing of one of the ignition coils was warped and damaged, it seems to still allow the coil to fit properly, and so far so good.
It was a huge pain in the ass, lots of yourube videos, lots of trips to Canadian tire for tools, and in the end I did save a tiny bit of money. But next time I need to replace the ignition coil, I will know what to do.
The tool that made the difference to get the boot out was the long pick like tool (kind of what oral hygenists use to scrape your teeth). The curved end is good at grasping the boot and pulling it. Also, a flashlight was important to see exactly what I was doing.