I'm shooting blind here because I don't have the conversion item. But most likely this is what you have to do.

-- Select the shorts in the scene.

-- Choose Object > Copy Morphs From

-- When you are prompted to select the item to copy morphs from, select the Fitting Suit PROP (you may need to use a drop down menu to select it)

-- There should be a morph in the fitting suit named LF 2 or something like that. But I suspect there might be other JCM morphs in there as well. It might help if you provide a screen shot of the morphs that are included.

-- In any case, after you copy the morphs, you want to select the shorts object, and "dial in" the LF2 body shape morph. You should see the shorts change shape.

-- With the shorts selected, choose File > Export > WaveFront OBJ.  Export the LF2 shorts object to the location of your choice (check the LF2 readme perhaps it makes suggestions). Make sure to name the object differently than the original. Perhaps the original filename with LF2 appended.

However, note that this OBJ file is still a PROP, it's not a conforming figure like the original shorts were. Not having the instructions for the conversion kit I'm not sure if it explains where to go from here --- and if you think you've had questions up until this point ... you're in a whole new, and very advanced, ball game with creating conforming clothing 8-)