From Lake Garda, you could head west and go to the Aosta valley. Great riding there (Pila, La Thuile, etc.). Then either go through the Mont Blanc tunnel to Chamonix or cross the col du Petit Saint Bernard into the Tarentaise Valley (Les Arcs, Sainte Foy, La Plagne, etc.). From here, head south to Les 2 Alpes, Alpe d’Huez, etc. then on to Provence and the Maritime Alps.
Give me a shout if you want some info on the riding round here.
The White Room – Tarentaise Valley Mountain Biking
EDIT: Hadn’t noticed the finishing in Portugal bit! From Provence, head to the Pyrenees, into Spain and down to the Sierra Nevada, then over to Portugal. Dammit, sounds epic, I want to do it myself now!