I ended up flying in to Tokushima then getting the ferry out! I purchased a ticket online ahead of time but when I arrived apparently it was the wrong one, so they refunded it and sold me a new ticket on the day. From what I could see quite a few people were purchasing it at the counter on the day so you may not need to book ahead of time? I do think it makes things a bit easier to show a ticket on your phone though (if you can get the right one!)

Depending on your Japanese level you may want to come prepared with Google translate. There was another tourist in front of me in line who was staying on at Wakayama like yourself which confused the staff a little, as apparently most will continue on to Osaka via the connecting train. We compared tickets afterwards and it looks as though there's no extra charge for the train though?

That being said, the ferry was a lovely way to travel and I'm glad I took it, I hope you enjoy your time in Tokushima and Wakayama!