Faro is only 280 kms from Lisbon and linked by a good toll motorway. It is therefore only 2,5 hrs drive.
I would suggest that if you do want to do something en-route you should consider the following:
Faro to Castro Marim.
Castro Marim to Mertola
Mertola to Beja
Baja to Evora
This will give you a taste of the interior of the Alentejo region. It will take about 5 hours. Certainly stop and walk around Mertola
Evora is a Unesco World Heritage Site. Hotels there include the IBIS. There are Roman Ruins, old churches etc. Spend the night there.
From Evora, Lisbon is only a 2 hours run.
