You can get the needles seperately-no problems at all. They are all packaged on their own and are all free on the schedule so medicare will still cover them. Splitting MMR would be another story however. So long as you have them all done before 18 months there are no problems with centrelink/child care rebates etc either. As you can see, I took longer than 18 months but I signed a COF when we went for the very first vax. I was lucky as the lady checking us in gave me one and had the nurse sign it as I was varying from the schedule so it was easy-peasy to get done and I've never had any hassles with immunisation payments.
I have done all my son's vaccinations at the free council clinics so I just rock up, tell them what needle we are there for and he just has that one.

Persephone- I'm looking forward to hearing your varied schedule. Glad the appointment went well.