I agree with valygrl about long flat distances in some parts of Australia. Planning to use the train for part of your trip is a great idea.

I think southwest WA is not to be missed if you are flying into Perth, it is a beautiful part of the world. The Margaret River area (beaches south of Perth, wine area and surf beaches between Cape Natrualiste and Cape Leuwin, Hamelin Bay), the tall timber country and the southern coast are great. You could cycle to Albany or maybe Esperance, but I'm not sure where you can pick up the train to Adelaide - I don't know if you'd have to bus back to Perth, or if you could get to the train from Albany or Esperance.

In SA I only know the area around Adelaide. (BTW if you like steak make sure to have a meal at Gaucho's in Adelaide, it is incredible). McLaren Vale is a wine area easy to get to using the suburban train and a bike. The Clare and Barossa valleys are a bit further. Kangaroo Island is also popular but I don't know much about it. I'll let others advise you about getting from Adelaide to Melbourne. The Grampians are probably not a viable side trip on reflection.