With the pilot shaft you will have to get a different flywheel nut or modify the one you have if this can be done. You should have gotten one with a standard shaft. I run pilot shafts with my Savage and Buggy but on my MT I run a standard shaft. It is not big deal! Here is a TZ with a standard and pilot shaft as comparison.
http://www2.towerhobbies.com/cgi-bin...?&I=LXHLW1&P=0
http://www2.towerhobbies.com/cgi-bin...?&I=LXHLV6&P=0