You can do the Customs/AQIS/Port clearance yourself, its a bit time consuming and can involve some running around - allow a day. Customs are usually very helpful and are not obstructive, one of the few Govt. Departments that actually seem to want to make things happen.
Customs and AQIS processes are usually handled in the same offices and you just hand over the carnet for stamping and the fees. Customs/AQIS will then tell you a time for inspections (Customs may inspect, AQIS WILL inspect), you have to be present for the inspections.
The costs - Customs - sorry dont have a clue. AQIS about $180 per inspection depending on where the inspection is done.
Other port costs that most people dont understand - the shipping company (the ship) charges a fee which pays for part of their costs for using the port. The Stevedores (the blokes who unload the ship) charge a fee. The transport company that moves your bike to a Customs warehouse charges a fee. The warehouse charges a fee to unpack the container. With a shared shipping container you pay a % of the fees usually based on the cubic measure of your bike or crate.
The costs can escalate very badly if AQIS inspect the bike and it fails. Most transport/warehouse companies do not have AQIS approved vehicle cleaning facilities and the bike/crate (sometimes the shipping container as well) has to go back to the (usually) port's vehicle cleaning facilities.
Goto the AQIS website and download their cleaning standards so that you know what they expect.
I was talking with a New Zealander last week and he paid over $2500 to clear his Nissan Patrol in Brisbane about 2 weeks ago. He broke about every AQIS rule going (full water tank, visible dirt, plus others) and got well and truly stitched up because of it. He was forced to pay for the removal of carpets, door trims, etc. for vacuuming and washing. I think AQIS enforced the "clean as new" rule on him. The AQIS costs were only a few hundred dollars, the other charges were horrendous.