No requirement to arrive any time. Once the visa is issued you have 5 years of validity to use it. You can wait 4.5 years to enter Thailand if you want.
When you got your extension, did the immigration officer put a slip of paper in your passport that gave you a new 90-day report date that was 90 days from your extension? If not, then your next report is due 90 days after your previous report.
no. Online reporting can only be done before the due date. And some offices only accept online applications from 15-7 days BEFORE the due date and reject any applications after that. If it's past the due date it must be done in person, but no fine until 8 days after.
The fine starts after the 7 day grace period. And if you get to the point of being fined, you should just hold off until the next time you need to go to immigration. Because the fine is the same 2000 baht whether you are 8 days late or 8 months late.
2 times in a year is probably okay. But you need to be more worried about immigration in Thailand than you need to be worried about the embassy. They will not let you stay in Thailand for a long time as a tourist. You risk being denied entry after too long.