We had a flight into MXP last May and it was on time. As previously posted, passport control and customs went rather quickly. I do not remember the exact times. Other items to consider would be: do you need time to find an ATM; the wait time for the Malpensa Express; time to check luggage at the hold luggage at Milano Centrale; the time to get to the Last Supper (at least 1/2 hour).
I would work this backwards. What is the latest time you feel comfortable with in arriving in Rome? Find the latest train that meets your criteria. Then give yourself about an hour to get from the Last Supper to your train (remember you will have to pick up your luggage). Now what time would you have to be at the Last Supper. If I remember correctly you have to be there 30 minutes early. How much time do you now have from your flight arrival time. Myself, I would want at least 3 hours especially if you have not been to Milan before. Getting around a strange city always slows things down. Then the trick is to get Last Supper tickets in the available time window. They are hard to get (do a search, there are many threads on this subject) and for 5 people will not be easy. Oh, somewhere in there I am sure you are going to want to stop for a quick lunch, another 1/2 hour or more.
Also, remember you will be doing all of this in a jet lagged state of mind and body.
If you really want to see the Last Supper I would plan to stay in Milan at least one night and buy tickets to the Last Supper for the next morning. You might have to split your group. It sure would reduce the stress.