Everything is possible - but!
OK its certainly possible to transfer the bits from one crankcase to another (assuming Suzuki haven't made any significant internal changes between your original model year crankcase and the 2006 doner engine) but before doing it:
- are you a competent / experienced bike mechanic. Splitting an engine to the level required to do this, whilst not rocket science is major surgery and not a task for the inexperienced or faint hearted.
- related to the above do you have access to a good workshop and a comprehensive set of tools (including torque wrenches, flywheel puller, clutch holder etc).
- assumming you say yes to the above then consider this. The crankshaft bearings and the gearbox shaft bearings are all press fit into the two halves of the crankcase. To do the swap the internals successfully you have to either remove these from the new engine (which is often an easy way to damage them - especially as some of them are fitted to blind holes so removing without damage is near impossible) or put the shafts from the new engine in new bearings in the old crankcase half (I haven't priced this but it maybe expensive because at least some of these bearings are usually specials only available from the dealer). The third alternative is of course the new shafts in the old bearings - but that would be very dangerous unless you are certain they are good.
I presume you want to do all this because you suspect it will be almost impossible to get the Australian authorities to update the database/rego papers without inspecting the bike which is of course impossible. I have a NSW bike in the UK at the moment so I appreciate the problem.
If it was me:
- I would only do the swap of the internals if I had access to a good workshop, tools, time and some spare $ for parts. Then I would do it because I am experienced and because I want to see the internal state of the new engine in case there were any problems.
- without tools, workshop, time and $ I would not do it. Instead I would sit on the computer and produce an official looking form recording the change of engine numbers and get it stamped by anyone you can (local garage, justice of the peace, anyone who can help it look official). Also keep all paperwork associated with the purchase of the engine etc..so you are able to justify it all to border guards etc
An alternative would be to file the original number off the new engine and stamp the required one on. However I suspect it would be hard to do this well and might end up looking dodgy.
My final comment is I don't believe anyone ever checked my engine number from Russia through to the UK.