The tuner just needs the (correctly wired) extension harness, nothing else - except the antenna cable.
IMHO there is no reason - except a sloppy install - for there to be a bunch of capped wires (unless possibly if the factory radio integrates a lot of other functions). A few yes, if you don't use functionality like the dimmer and celllphone muting, but not 'a bunch'. The cradle comes with an ISO connector and the mating connector is supplied too. A proper install would just splice the mating connectors wires to the cars wiring, or to an adapter specific for the car in question - Tony has a good description of this in the FAQ at
http://www.riocar.org
Unfortunately it is likely that the installer at Best Buy cut off the ISO connector and then started splicing directly...
I wouldn't be surprised if your suspicion that they f*%¤#d up the install somahow is correct.
/Michael