I visited the campus last year and it was great. I applied ED to engineering with a 3.59/1370 so im about in the same boat as you regarding acceptance/denial chances.
The only thing bad I can think of to tell you about the school is that it is not located close to any big cities or cultural centers, but this isnt necessarily a bad thing and didnt stop me from applying early decision.
In my opinion you should apply early decision for all of the reasons you listed. I also had some issues with my application and through calling admissions I figured out how to make changes to it after submission. Follow the directions carefully on this page.
Application Changes -Admissions- Cal Poly.
You might also want to call admissions tomorrow to confirm that you can change to ED still before you send the email.