If done correctly, the differences between a 1969 RS and a non-RS car are many. I have an original 69 RS so I do not have any experience with the conversion kits, but the RS variations from the "standard body" for 1969 include the following and your conversion kit should address all of these issues:
Different outer fenders, different inner fenders, different grille and trim, different grille, fender, and tail panel emblems, hideaway headlights assembly including articulating mechanism to connect them to the vacuum canisters, inner and outer headlight door covers, vacuum cannisters, mounting brackets for the vacuum cannisters, vacuum reservoir, relay valve and the associated vacuum lines, different headlight switch with vacuum hose connections, different windshield wiper switch (2 dentent positions, first detent routes water to the windshield washer nozzles, second detent routes water to the headlight washer nozzles which spray water on the headlights), headlight washer nozzles, diverter valve on the windshield washer pump, water tubing from the diverter valve to the headlight washers, mounting in the front header panel to accomodate the headlight washers, diferent bracket/location for the windshield washer bottle, and the other items in the Style Trim RPO that are a part of RPO Z22, the RS package.