I believe you can put the stock shifter back in, and it will use the bushings from the short shifter kit. When you take out the stock shifter you have to destroy the plastic bushings to get it out, and they are replaced by a different replaceable style that come with the short shifter. If you don't like the short shifter then you can put the regular one back in. Check this 101 Projects article for more details:
Pelican Technical Article: Installing a Boxster Short Shift Kit (SSK) and Replacing Boxster Shift Bushings - 986 / 987