It turned out to be multiple things combined to resolve the stalling issues. We took it to Happy Days Marina in Port Clinton, OH. Tim, Brad and their "Yamaha Rep" (I did not find out his name) there did a fine job diagnosing and repairing the engine.
1. Replaced Throttle Positioning Sensor
2. Replaced stuck open thermostat
3. Cleaned and de-carbonized the engine & fuel injectors
4. Changed oil & oil filter
5. Replaced all 4 spark plugs
6. Tuned, sync & balance
7. At the Yamaha Rep's recommendation, we replaced the prop with the "correct" prop which allows the engine to achieve the proper RPM's at Full Open Throttle.
$741 and a couple weeks later,... we have a properly working engine that does NOT stall at idle anymore; and pushes my 21' center console Sea Fox-Bayfisher above 40 mph. (old max was about 30-35 mph) Big difference! I am very pleased with the results!