1) Lack of Cinematics
For an RPG, you really should have cinematics added in your scenario. It's the best way to effectively introduce your scenario's goals and the best way to start it. If you don't have Reyk's editor, I highly suggest you get it. You might also want to add cinematics for when you have in-game dialogue and to end your RPG.
2)Trigger Crashing
I also know that I could have done shop trick triggers, but my computer started crashing @≈80 conditions and effects.
This isn't an issue with the amount of conditions/effects. A lot of scenarios will run hundreds or thousands of triggers will lots of effects and conditions within them (my own included). If you're having issues with the game crashing, it's because of a trigger conflict within the scenario. That's where you'll need to figure out which one isn't working.
3) Kill Triggers
Now that I've actually looked at your scenario, it's a single player RPG right? If that's the case then you can actually use the condition "QV Player Dead Units" to track what units you've killed.
So you're off to good start. Add in some cinematics, some more triggers for game play, and I think you'll be in a much better position.
If you want an example of a great RPG, I've included Zelda which is probably one of the best RPG's created for AOE3. You should be able to get some ideas from it.