I trained at eagle. Got there with almost 5,000, mostly twin time and some serious IFR in the northeast. They just about ate my lunch. I consider myself lucky to have gotten through. How any 1,000 hour CFI gets through is beyond me. Many flowbacks from American have failied that course. Believe me, you can be an excellent pilot and not make it through there, and those Embraer sims are very unstable single engine.
I have no doubt that you are a good pilot, and I applaud you for trying to make such a huge jump. I highly, highly reccomend you do a little 135 work, maybe some check hauling. It will introduce you to a new regulatory einvironment, as well as sharpen your IFR skills. After a year of scheduled 135 at night, you won't be afraid to look any pilot in the eye.
Keep your chin up. I consider you lucky to avoid being an Eagle FO. It's not a fun job.
I think the EMB sim is pretty easy on one engine. I don't know the exact numbers, but I'd gues Eagle has at least an 85% pass rate for new-hire training and that includes all backgrounds and experience levels.
Aside from the long upgrade and low staffing, I don't think being an Eagle F/O is any worse then any other regional.