I'm not sure but I think the answers are:
1. Yes on the combo ticket, per the Port Authority website, but as you mention in the next paragraph you can also "save" the dollar fee by just buying an ordinary Metrocard for two with the 11% bonus. I don't think there are any cards available at merchants to save you the fee.

2. Yes but they may make you go up to the next nickel ($9.05) or something, I'm not sure.

3. It appears from the MTA website (http://web.mta.info/lirr/about/Ticke...#onboardtrains) that you can pay the step-up fee on board without the on-board fee for a whole new ticket, but you do have to round up to the next dollar.

4. If you are light on luggage and watching each dollar and not averse to transferring to a bus in an unfamiliar area and willing to use up some more time, consider taking the AirTrain to the A, then the A to Far Rockaway (away from Manhattan) instead, and then taking the NICE (Nassau County) bus #33 to Long Beach. The subway is $2.75 and the bus is $2.75, both payable from a Metrocard with sufficient $ on it, and I am pretty sure there is a free transfer both ways but you may want to have coins available just in case.