There are three ways to travel between Faro and Porto:
Air
There are no direct flights between Faro and Porto.
TAP, the national airline is the only operator on the route. There are several flights per day from Faro Airport to Lisbon where there are connecting flights to Porto.
This is usually the most expensive option and not much quicker than train unless you get the very early morning service.
Rail
Since late Apri 2007l, CP - Portuguese Railways has been operating a summer schedule with two direct Alpha Pendular high speed trains per day between Faro and Porto via Lisbon.
You can download the timetables from my blog as the url is very long:
Go to:
http://barlaventostravelblog.blogspot.com/
Scroll down on the right until you come to:
Algarve & Portugal - Travel Transport Links
Click on:
Porto - Lisbon - Porto Train Timetable
This will allow you to download a timetable in pdf format which shows not only Lisbon Porto services but the two through services from Faro to Porto.
Transit time will be +- 6 hours.
Bus
For Bus:
Have a look at www.renex.pt for services. Timetables are downloadable on the left under Horarios.
There are 6 services a day with a transit time of 4 hours to Lisbon Gare Oriente.
The same company then runs about 10 services a day from Lisbon Gare Oriente to Porto. transit time 3,5 hours.
Buses leave Faro from in front of the bus station and tickets can be bought at the RENEX office opposite the bus station..
The bus will probably be the cheapest, but the train will not be much more.
For more info also see:
http://www.solpraiaferias.com/index.php?content=cheg_en
http://www.algarvebus.info
