First thing you may want to think about is whether you want to see the salt flats from either Salta (i presume thats why you want to go there) or on a 3/4 day tour from San Pedro De Atacama,Chile into Uyuni,Bolivia.
Personally i would skip out Northern Chile and spent abit of time in Bolivia.I was never going to go to Bolivia and im really glad i did.Bolivia is a fantastic place and theres the Pampas Tour which is amazing and cycling death road.
It all depends on where you fly into and fly out of and what you want to see.
Chile i wasnt impressed with too much to be honest.The people just didnt seem as nice there as they do in Argentina.
I only really liked the far south like trekking in Torres Del Paine and Pucon and then the far north in San Pedro De Atacama.
Santiago i disliked probably more than any place ive ever been to and due to a national holiday i got stuck there for a week.It was hell and every bus in every direction was booked.
The way i did it was
Lima to Cusco (Fly)
Cusco to Arequipa (Bus)
Arequipa to Puno (Bus)
Puno to La Paz,Bolivia (Bus)
La Paz,Bolivia to Rurrenabaque (Fly)
Rurrenabaque to La Paz (Fly)
La Paz to Oruro (Bus)
Oruro to Uyuni (Train)
Uyuni to San Pedro De Atacama,Chile (4 day tour in jeep)
San Pedro De Atacama to La Serena via Antofagasto (Bus)
La Serena to Valparaiso (Bus)
Valparaiso to Santiago (Bus)