You are going to need quite a few cold start cycles with at least a few 15-20 minute highway drives to try and see how many monitors you can get to set.
Usually the Evap and Cat monitors are last to set, however, if you recently had any codes for problems, these monitors usually take longer to set.
Also your exhaust leak could cause your to trigger Cat Efficiency codes from time to time.
You may have 1 lazy post Cat O2 sensor, but I would not get too worried about this yet.
You may need between 150-200 miles before you have monitors set.
Also make sure your engine is going into closed loop and staying in closed loop.
Your questionable thermostat may have caused the engine to drop in and out of closed loop too often.