5 days in perth

That would be a very long five days if you were to fit that all in!
Perth and Fremantle could possibly fit in one day depending on how much you wish to see or do and can be done easily by public transport.
Rottnest Island is a day trip. Ferry approx 8.45am and return 4.25pm. You could do this depending on the weather - Wouldn't be very nice if it was forecast to rain the whole day!
Swan Valley - You can get to Guildord (the beginning of the Swan Valley) by train but from here you run out of options. You can book a shuttle around for $30 for the day to take you around if you didn't wish to do a tour. This would be a day also unless you joined an afternoon tour.
The Pinnacles - You can technically get here by the Greyhound bus (not public transport) for around $50 but these do not run reguarlly and I doubt you can do a return trip in the same day with this service. I suggest joining a day tour for this one (it is over a 3 hour drive each way).
Margaret River is approx a 4 hour drive. Once again not a great day trip with 8 hours of driving!
If it were me - I would see Perth and Freo in one day, a trip to Rottnest Island the next (weather dependent), join a day tour to the Pinnacles and spend the last 2 days in Margaret River. No need to do BOTH Margaret River and Swan Valley in this time. You can get a bus to MR. (www.transwa.com.au)
Erica