Do you know how long it has not had an air filter for?
I would also be changing the oil and filter once you get the air filter in. As an explanation, the air filter will create a slight difference beween the air pressure outside the bike and the air going into the carbs. This pressure difference will assist the carbs in getting fuel into the engine. Without the air filter the air/fuel ratio approx 14:1 is going to be running with too much air, therefore the mixture wont burn properly.
Thats why carbs/EFI need rejetting/remapping when the air intake or exhausts are changed as this changes the air fuel ratio.
The above is my basic understanding of the process.