Hi all
Just bought a shift linkage cover put over to see how it looks(didn't attach) now I can't shift past 2nd and the heel shifter is hitting the floor board WHA HAPPENED?

 

Your shift linkage is probably shorter than the old one. Could be when you installed the new rod you screwed both ends in further than the old one was or the new rod is just a little shorter. Loosen the jam nuts on both end of the linkage and unscrew them 1 turn eachand retighten. Orif all shifts well just take a allen wrench and take the foot shift arms off and rotate them one notch counterclockwise or until they are positioned where they are comfortable for your riding style.

 

After rereading your problem I probably misunderstood and answered wrong, if so, sorry. Is the shift linkage cover over the arm on the tranny or on the linkage itself?