I got a definitive answer on the fuel smell and backfiring.
I guess the dealer didn't want to say anything bad about the MoCo, so he couldn't tell me the 110 in stock form performs like that.
I told them that I knew the motor wasn't breathing right and ran hot due to the EPA restrictions. I added that I knew it wasn't MoCo's fault, but the EPA overreacting to what little emissions bikes put out. After that statement, I asked what I could do to 'help' the motor. First words out of his mouth were "SERT and true duals". They went ahead and reflashed the ECM to see if the backfiring would stop. 450 miles later, it hasn't done it yet. But, I can really feel the heat pouring off the motor at 60MPH. I had to sit at a long-winded traffic light and it all of a sudden sounded like it was running on one cylinder. I found out today that's exactly what it was doing. It's part of the latest flash. I didn't know these motors could cut back when they get too hot.
They helped me out on the price of the SERT and exhaust. $300 for the SERT and $470 for V&H pipes. SHould be here sometime this week...just in time for the 1k service. The service and dyno time is going to cost at least $600. Thankfully these bikes already come with the SEAC, or that would be yet another costly item I'd have to buy.
As a side note, I was informed that they were currently in the process of replacing 3 other 110 motors due to overheating. Two were from SEUCs and one was from a Dyna. All three were stock and none had over 2000 miles.