I'm not a real world pilot either but here's my input...opinion.
1. I don't know about the ATR72 but I have flown a/c that will vibrate if you are in an overspeed condition. If you are not overspeeding and think the vibrations are being caused by turbulence you can request a different altitude if ATC is online. If no ATC is available you can change altitude at your discretion and refile your FP as Todd mentioned above.
2. For choosing altitudes, first you must follow the rule of flying even or odd altitudes based on your direction of flight. In the real world many factors are taken into account (a/c weight, winds, most efficient for a/c, etc.) but the primary one is the expected winds aloft. You want the most favorable winds for the majority of your flight. For us "virtual" pilots it's simply the direction of flight (and if you are flying international some of the Jetways will define an altitude range).
3. Sorry don't have any answers or input for this one.
4. For ILS approaches, if you have ATC they will vector you to the ILS localizer which normally means deviating from the last few waypoints on the STAR. So at that point you would have to switch to HDG to follow ATC's commands (unless you are start "hand flying" at that point). If no ATC is online and you have the appropriate STAR and Transition selected you can switch from LNAV to APR a little before reaching the IAF.
Normally you want to establish on the localizer below the glide slope. When the slide slope becomes active the general rule is you lower your gear when the glide slope indicator is one notch above the center line. Deployment of flaps is always based on speed and is dependent on a/c weight. The FMC will provide appropriate approach and landing speeds. You should plan to cross the threshold at landing speed.
5. Cruse speed for the ATR is difficult for me to answer. I'm sure there is a single answer for real world a/c but for FS I've had ATR's that would do 300+ knots and some that would not com anywhere close to it. It all depends on the virtual a/c modeling and how close to realistic it is. For virtual a/c as long as you are not in an overspeed condition you are fine. I can't answer for real world a/c.
6. I think it is ok for the ATR to fly Jetways as long as it can get high enough to meet Jetway restrictions, however I don't truly know the correct answer to this question.
7. Altitude selection was addressed in #2. If you want to be as real as possible you can go to
www.flightaware.com and enter your flight number or the departure/arrival airports and see real airline flights for that trip. It will provide routing, SID's, STAR's, and cruise altitude flown by the real world flight.
8. This was answered by several people already.