Low Oil Woes

I bought a used 2006 Tribute with 57,000k, 4cyl in November, 2010. In early January, it developed a knocking sound, like tappets or valve lifter clatter. Took it to the dealer, Metrotown Mazda, where they listened to the sound and said, yes, that sounds bad. We'll have to take the head off to see what's what, but it's not good. I didn't buy an extended warranty (the salesman had promised me that it had a powertrain warranty until July 2011, but I, gullible guy that I am, didn't get it in writing).

So, I decided to take the car elsewhere for service. But before I did, I checked the dip stick: NO OIL! Put in 3 litres then whipped into Mr. Lube for a flush. Thought i had a leak, but no drips showed. The Mr. Lube teckie showed me the air filter: clogged! Showed me the fuel filter: clogged! Obviously, the dealership didn't do a service check on the car before they sold it.

I'm at fault, I know. As soon as I drove it off the lot, fluid levels became my responsibility. Phoned the Metrotown Mazda service guy and he agreed: my responsibility. Anything else I can help you with today sir? AARRGGHH.

Anyway, here's my question: After getting a flush, new oil, new filters, etc., the terrible knocking noise has decreased in volume, but it's still there. Have I done irreparable damage to the engine? I've driven it about 3,000k with very low oil. And what's likely to be making the terrible noise? Motor bearings? Any advice would be welcome. It's not tappets or lifters, but something more nasty, I'm sure.