Heaps of people from Canberra who frequent this forum have engine conversions the same/similar/very different to this.
My car was originally engineered as a 4AGZE (now a 4AGTE)
The most commonly used engineer to gain your certification from in Canberra is John Wilson (he is in the phone book and lives out near Burra or something I think he trades as KZ Engineering or something like that). A very reasonable guy. You will be looking at anywhere from about $600 - $770 for the certificate depending on what he is certifying.
He may or may not require you to perform a brake upgrade in order to pass (he will perform a brake test though so make sure they work well. I think his current test requires 10 stops from 100 km/hr which he does out at the old drag strip near the airport), this is something you should check with him as it varies depending on the car and engine being fitted.
Once John has passed it and provided you with all his documentation you then book yourself in for an inspection at the Dickson rego station. You will need to ring up and book in as they only have certain days on which they inspect modified cars. At the pits they will be checking the usual roadworthy stuff that they check on any car and will probably do another decibel test and the brake test on their roller thing. Make sure you take a COPY of your engineers certificate as the rego station will take that from you and keep the copy on record (no doubt they lose it or something though).
If you want to pass through smoothly make sure all your factory emissions gear is hooked up when the new engine is fitted e.g. crank case breather, carbon cannister, catalytic converter fitted etc. Make sure it looks neat (not bodgey) and you should have no probs.