Are you sure? I'm pretty sure the holes are in the same location as the earlier flares. The screws you see on the outside of the flares are fake. I did the toyota tape like Sea Bass but thats cause my 04 didn't have any flares at all. First I bought some 98+ flares but decided to go with the 06's cause thats what I really wanted. I looked and compared the 98 vs 06 and I thought the holes were in the same place but I didn't pay that much attention.
I bought mine from a discount online dealer. They were like $70 a piece I think. I couldn't find a set at any salvage yards and every salvage yard that I talked to said if they had them they don't sell them separately. They go with the fender/bed they're on.