there is an easy way...
the 05 bike uses a 20mm axle and the 06 has a 25mm axle so all you need to do is use the 05 axle and have a sleeve made to go through one side of the fork leg.
Right then, before we start...
Left and right as you sit on bike, OD = outer diameter, ID inner diameter
All rears 04 -09 interchangeable (colours vary), all using 20mm spindle. 06 has different caliper carrier though.
04/05 front: 20mm spindle. 04/05 forks - left side 25mm hole with captive nut, right side 20mm hole for spindle to go through.
06/07 front: 25mm spindle. 06/07 forks - both sides 25mm holes - uses 25mm axle all the way through with a nut on the outside left.
Both spindles go in right to left. The key to making this work is the fact that both fork left side holes are 25mm.
So using this information, to put an 04/05 wheel into 06/07 forks we need an 04/05 spindle because a 25mm 06 spindle will not go into a 20mm 04 wheel axle hole.
The left side 04 captive nut goes straight in 06 left fork bottom (both 25mm), so the only problem is the right side as we have a 20mm 04 spindle in a 25mm 06 fork hole.
Go to a local machine shop and have a shim/bush made up as attached picture, this will take up the slack around the axle on the right side. The split is important (can be cut with a hacksaw after turning) and you should align it with the bottom of the forks as this will allow the pinch bolts to grip/clamp the shim onto the axle. Specs - OD 25mm, ID 20mm, Length - 39mm.
SO TO PUT AN 04/05 WHEEL INTO 06/07 FORKS YOU WILL NEED AN 04/05 SPINDLE PLUS THE SHIM.
or to put it another way this is from zx10r.co.uk
You can change the bearings in an 04/05 wheel for ones with a larger ID (25mm instead of 20mm) to allow an 06 spindle to go through but the bearings will be thinner, (as in left to right) thus needing new wheels spacers both sides to take up the slack and centre the wheel. 06/07 bearings will not go into an 04/05 wheel as the OD is larger. (06 wheels have larger hubs). This method will need two new bearings, two new grease seals (ones with larger ID), and new left and right wheel spacers. All in all more costly and the thinner bearings have a lower load rating. (think spacers would need to be 3mm longer to go deeper into wheel - compared bearing sizes and thickness a while ago when working this out.)
As for the 06/07 front, it will go straight in an 08/09 as the both use 25mm axle hole, but axles and fork bottoms are different. 08/09 forks have different bottoms, axle middle part is 25mm but has a larger (30mm?) shoulder and captive nut, like a larger version of the left side on 04/05 forks. Only problem here is disc sizes 300mm vs 310mm.
Going backwards and putting a 06-09 25mm axle hole front in 04/05 forks would need the bearings and seals changing for 20mm ID but then these would be thicker so spacers would have to be trimmed, OR perhaps you could sleeve down the 25mm hole (all the way through the wheel, including spacers) to 20mm to allow 04/05 axle to fit.
Any questions pm me if needed and i can give you a call. will be putting real pictures up next week to make this more clear.