The time you want to arrive is up to you. I see the first bus to Stresa is at 9:00 and the next is at 11:30. If the flight is on time you could be at the bus stop within one hour from arrival, but I’d rather get there with the earlier flight, all other things being equal. That would give you a cushion in case of a flight delay and in case of no delay you can relax, have breakfast at the airport, freshen up at the restrooms and relax. Also you can enjoy an extra 2.5 hours in beautiful Stresa. Also, if you opt for the train, I wouldn’t bother to back track all the way to Milan to get back to Stresa. The better option is to take a taxi from the Malpensa airport to the Gallarate train station and from there take one of the numerous trains to Stresa. A taxi can take you to Gallarate in 15 minutes. The train from Gallarate to Stresa is about 30 minutes. Another, train option is to take the train from the airport to BUSTO ARSIZIO, then at Busto take another train up to Stresa (that train will stop in Gallarate on the way to Stresa). This option is cheaper then the taxi to Gallarate then train, but it will take a bit longer (about 1h 15min). In any case there is no need to go all the way to Milan, you can change the train in Busto Arsizio.
For the return flight from FCO from Prati/Vatican I would probably take a taxi for convenience, especially if you have luggage. The taxi will take about 35-40 min depending on traffic. However the taxi costs 50€ flat rate, so if you prefer the public transportation option to save money you can take the metro to Termini and then the Leonardo Express train to FCO. It might take you about one hour, all things considered, unless your accommodations are far from the closest metro stop.
You should try to be at the airport about 3 hours prior to departure or at least 2.5 hours prior. So you decide on the best time for you. I’m not a morning person, so unless I took the taxi, I would probably go for the later flight.