The 05 and the 06 are identical as engines.. the difference is with the previous model.
Also, it is not correct to say that the 05 has the 04 S engine. It is slightly different. The 2005 models are the ones that have been revamped the most, 2006 didn't get any mods from the previous year.
A dyno chart that show the diffrences...
http://www.moto-one.com.au/performance/99905mod.html Ciao
Brogins