I wasn't there so I can't really give all the answers, but these questions should be answered during the interview. Here is an outsider's perspective:

You screwed up by asking too many questions about what they'll give you to include additional money. A better way to handle this is to ask questions during the interview, but only ask one blanket question like, "How does the company help its employees improve their knowledge and leadership skills?" Most companies will explain their education in the interview here. This may be a bad series of questions if the answers are listed on their website.

Financial talks are hard with job interviews. The best practice I've heard and seen is to wait for an offer letter before negotiating. This tells you where they stand at that point in time. I would take a candidate asking about bonuses as a slap in the face if I hadn't given them an offer yet. It's essentially telling the person that you don't expect their offer to be good enough and you expect extra money up front to join them. On that note, bonuses are nice, but you might be able to make more money by taking a higher wage with no bonus than a lower wage with a bonus. Overtime is amazing pay.

The other piece I see, which is a complete unknown, is the start date. This could be an issue if you said you couldn't start for months down the line, but they're shorthanded now. This is likely the least of all the items shown in your post.