Glad to see you've got it sorted.
It does sound like you have otitis externa, a very common condition affecting the lining of the outer canal of the ear.
I can't see any reason why this would affect your abilities as a pilot, (see the ame blah blah), some ent folk see this as being more of a skin condition, rather than an ent condition.
The key to eventual cure lies in keeping the skin in the canal dry, follow my tips above.(Vaseline/cotton wool). If the discharge gets pongy, go and get a prescribed antibiotic/or antifungal (drops), if the itching is unremmitting, try prescribed steroid drops in the short term, see an ent quack for suction and packing if no success.
Don't ever forget your GP
He's probably a nice bloke who can at least give you sound advice or point you in the right direction if thing's don't improve.