How can I fix my Gilera DNA 125?

After a particulary wet day I was riding home when the bike started to lose power and then pick up again. I was riding at about 7500rpm when it would drop suddenly to the point where it would almost cut out but then it surge back up again (never moved the accelarator). This carried on for about 10 mins (2.5 miles) and eventually it did cut out. i tried to start it but it wouldn't so I left it for another minute and it started up fine but then continued to surge and lose power. I thought it might just be the rain getting in somewhere but I left it over night in the garage to dry. Next morning it started up first time but still continued to lose and then regain power after driving ok for about 100 yards. I put a new coil and spark plug on about 2 months ago, is it possible that the air filter might be dirty and need replacing thus its not breathing right?