Did similar coverage last year. Pamukkale is quite far from Izmir so it might be hard to do a day trip. Here are my photos to help you plan what to focus : http://www.globalphotos.org/turkey.htm

Gallipoli and Troy are quite far from Istanbul - about a 4-hour bus ride I recall. From Izmir, it was about 5 hours. I thought Ephesus was more impressive so I'd suggest dropping Troy. Some Aussies are very keen on visiting Gallipoli. From there, you need to take a ferry across the straits to continue to Troy.