Some immigration offices align your 90 day report with the visa but if they did you would have filed a 90 day report at the time and they would have put a slip with your next reporting date in the back of your passport
The first one on each entry can't be done online, but if you are organised you should be able to do by post or you can get someone else to report on your behalf
The dependant visa as a spouse of a DTV holder is straightforward. You don't need an agent, just the details of your wife's DTV and details of finances
Your partner here on a Non-B visa for work is unlikely to be able to write a sponsorship letter for you to apply for a DTV. Best to have the money in the bank yourself, what else you will need will depend on whether you apply for soft power or workation. If you are officially married then you could apply for a Non-O visa as her dependant with no financial considerations. Check the embassy website you will apply through for their requirements, you don't need to email them
Yes you can apply, make sure you’re course is 6 months or more and be aware they can ask you how you will support yourself during the validity of the visa
I wasn't implying it was anything to do with covid but rather mentioned covid as the OP gave that as the reason he couldn't renew it when he should have.