For the in/at questions, either "in" or "at" can be correct. It depends on what you want to stress.
"At" refers to a specific time, At 3pm, At lunch, At the moment. So you can say "At the beginning of July" if you want to stress that specific point in time.
"In" refers to a non-specific time, or a duration of time. In July, In 2010, In the past/future, In the end. In daytime. So "in July" an means very much like "during July": In the beginning of January = During the beginning of January.
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It is the same for "in/at the end of the quarter" and "in/at the end of the year."
As for "on" in prepositions of time, "on" refers to a (specific) day or date. On July 4th, On Christmas, On Saturday(s), On my birthday, On vacation/holiday.