ergaster2: Same application process for both enroute and tower, I was simply asked when I got the offer which course I wanted to be placed on.
I think most of the time involved in the medical is CASA taking their time with paperwork. You will also be required to undergo a drug and alcohol screening for Airservices Australia. I also had a minor concern about the medical, but I rang CASA and spoke to one of the doctors who approves the medicals and was assured it would not be an issue. I would not try to start the medical process yet as Airservices Aus. will give you someone to help you organise it all, just their procedure I guess.
Also try not to worry too much about how you did on the tests, I felt exactly like that, that there were some things I could have done better. They are not looking for perfection, just testing whether you have the right aptitudes for the job.
Good luck and I hope you have some good news soon.