Dear William,
1. For hourly weather data, SAM assumes that the first row of data is for the hour beginning at 12 a.m. on January 1 and ending at 1 a.m. The TMY3 convention is for Hour 1 to be for the hour ending at 1 a.m. on January 1, so the two are equivalent. The time stamp for the first row in tables on the SAM results page is "Jan 1, 12:00 am" indicating the time at the beginning of the time step. You do not need to modify your file for SAM to read it correctly.
3. SAM does not read the minute information in the TMY3 file. For sun angle calculations it uses the midpoint of the hour (by setting the minute value to 30 for all hours of the year). For the new SAM CSV format, SAM uses the midpoint of the time step for the sun position calculation unless you specify values in a 'Minute' column, in which case it uses the minute value you specify.
Best regards,
Paul.