After spending days upon days of troubleshooting random enemy generation, I realized just how flawed this method was. It was fine for an endless single level game, but presented big problems for what I wanted to accomplish. And what I wanted, and still do, were timed events and enemy formations.
I scrapped the whole method, and researched using Time Lines. It's so simple. Why didn't I do this earlier? Well, whatever the excuses, I'm glad I made the switch. Time Lines have none of the issues that my previous method did. I was thus able to add all the enemy formations for the first level, and the boss fight, all in one day. Hurray for me!
Next I'll be finishing off the boss attack patterns, and then the first demo can be released! Stay tuned.