Joseph – As HaLevi said in the Daas Torah thread, I don’t need a Rov to tell me Shulchan Aruch, that an Am HaAaretz can do. What you need a Rov for is to interpret and advise/Pasken what you should do.
So yes, after he discusses what to to with his Rov, he can have a Minhag not like the Shulchan Aruch.