There's no way it could be installed for $1000. I'd steer clear of whoever quoted you that.
The ductwork is, I'm sure, already designed to accomodate an AC system. But by the time a shop buys and installs the condensor, the evaporator, the compressor, the new front pulley to drive the compressor, the idler that'll probably be required with the sddition of the compressor, the lines and brackets, etc. it's going to cost you. The $3500 quote is probably closer to the truth.