Lee..
What you are you trying to do with the 06 chassis?
are you wanting to put the 05 engine in the 06 chassis or just rebuild the 06 motor?
depending on what your overall goal is...here is my expierence with the 05/06
--if you want to put an 05 engine in the 06, you can do this very easy...just gotta change a few things over from an 05 also...engine will bolt in fine, you will need to change the ecu, hald the wiring harness for sure...you shouldnt have an issue with the oil tank and steering column (06)..since the 2 injectors arent really in the way, but wouldnt be much work to convert if needed.
dont put an 06 in 05 unless you got time, money and skills, lol..
this is what i did and its been SICK!!!
on my budget 900 build, i have an 05 bottom end with TM1...out on 06 cylinders...got custom upper injector plugs from indydan to plug the cyl injector holes..used 05 fuel rail...but the issue was with the steering column, the 05 column hits the upper injecor boss on the 06 cyl...so i cut the boss section off just enough to clear the steering post...and runnig 05 fuel pump 58psi regulator
the 06 OEM cylinders are ported from the factory and are the same as the 05 ported cyl that SLP charges $500 for...so i wanted to get the ported perf....running an Rk-Tek head with the SLP perf pkg ecu flash...and it RIPS...
depending on whats wrong with the 06 engine, you could go with an 05 bottm end and use the 06 cyl and do like i did above and have a solid sled with the relaibility and ease of the 05's 2 injectors with the 05 fuel pressue (58psi vs 116psi)