Basically dose yourself up with an over the counter cold remedy an hour or so before boarding. Unless you have serious flu symptoms (you'll know about it if you do) flying with a cold is uncomfortable but manageable.

I remember having a similar problem on the day before flying back from KUL once - my wife has a friend there who's a pharmacist and was able to get me some decongestants. Felt absolutely great on those, never better, and had a really great flight. It turns out that a major component of Malaysian decongestants is speed.