Where will passport/security/customs check-ins occur?

Your flight from Venice to Munich is a inter-EU flight. No immigration or luggage checks. You will, of course, need your passport and you will go through normal security measures just like you would at your local airport. Once in Munich, you will need to be in the correct location to board your international flight. This may require changing terminal buildings. Again, normal security check-in. Nothing different than if you were departing Boston-Logan for Europe.

Larry is correct. At Venice, your passport is only your ID and there is no immigration control arrive in Munich. They will stamp your exit visa departing Munich. Which means leaving enough time in Munich to change terminals and get your passport stamped. Depending on if you are on the same airline, you may need to reclaim your luggage and re-check it in Munich. That really would be the major time issue for the layover. I'd schedule at least two hours, if not three.

There is no customs or immigration between VCE and MUC. However you'll have to go through regular security in Venice before going to the gate (like you would in the US) and then again in MUC before reaching going to the gate to the US bound flight. If I remember correctly you'll be arriving at the same terminal (T-2) as your US flight will be departing, however the Munich terminal 2 is divided into Piers (North and South) and there is a check point before entering one of the two (don't remember). If your flight arrives in one terminal (there are 2 in Munich) and your US flight departs from the other, you'll be also traveling between terminals. In any case you will be going through security check again in Munich before boarding the US flight. The German Federal police will also check your passport (I don't remember if before or after the security check). If you are flying from Venice you are flying either Air Dolomiti (part of Lufthansa) or Lufthansa itself (no other choice) and connecting to a Lufthansa flight (or United) to the US (no other choice). In Munich you will NOT pick up your luggage checked in Venice all the way to the US. You'll see it again only when you land in the US. If you fly to Boston (since you are in ME), your Lufthansa flight to BOS leaves at 15:55. The LH flight 1909 departs from VCE at 12:55 and arrives at MUC at 13:55. Two hours will be more than sufficient for the layover, that's your flight to take. If you fly to EWR, the flight leaves at 15:30. Still enough time for you to select LH 1909 departing VCE at 12:55.

Thanks, all, for that information. It's very helpful. I am still checking various flights, including Delta from Venice to JFK, nonstop. But I'm not sure yet which flight I'll be taking just yet, that's why I needed the information you all provided. Thanks again.