Come to Cuenca for 3 months

Bryan,
My understanding is this: you get 90 day for every 365 day period on your passport alone. The extension is strictly a bonus. Remember, it's not a calendar year, but 365 days from when you enter. So, my understanding is that if you stay for 90 days ( not counting the extension ), you can't come back in country for 365 days from your original entry date.
That being said, these attorney's can figure out all the possible angles, and if you are really interested, I'd talk to an attorney, or the Consulate before you make a commitment time wise. But... I think an in country attorney will afford you better real time information than a Consulate agent in the US. I got some bad info from the Consulate in Mpls., and my attorney in Cuenca set the record straight. The attorney's in Ecuador deal with these issues daily. I would trust a reputable attorney in country more than a clerk in the US.
Good Luck,
Neil