Hi Davina,
Afaik, from Mendoza, going to Cusco via BsAs makes no sense at all, timewise nor moneywise.
Your best bet imo is bussing it; Mendoza - Santiago - Arica - Arequipa - Cusco. Esp. the road from Arequipa to Cusco is gorgeous, plus bus travel gives you plenty opportunity to acclimatise (there's no use doing that in Lima as you suggested yourself; Lima is pretty much at sea level
). The whole trip would take you 3 days approx, or 36 hours of continuous bussing.
Alternatively, flying from Santiago (LAN offers daily service directly to Cusco) may be an option. My guess would be that that's quite expensive (ran a quick check; prices are around 600USD), though flying from BsAs will doubtlessly cost you even more.
[ Edit: Edited on Feb 1, 2008, at 2:37 AM by bentivogli ]