flying in to HKIA arriving at 7.25am (cathay, from Australia) and need to get the ferry to Shekou.

First of all, I'd like to tell you that your time is totally enough to take the ferry at 09:00.

After landing, no need to go through the immigration. You can directly walk to Arrival Level, T1 and buy the ferry ticket at the Ferry Ticket Counter at Transit Area E2. There you need to show your luggage tag receipt and the staff will help you handle the luggage, so you don't need to collect the luggage on your own. After that, head for the Skypier to check your luggage and board the ferry.