Petski,i have exactly what you said. When i start the engine,the downpipe of cyl 1,run colder than the others.... The jet i'm talking about,is where is the yellow arrow i draw...(see pic pls).At my carbs these jets are completly blind..and i dont know if it sould be this way or not...i cant even find it at the Yam manual.
You now know where to be looking then, cyl 1. Please note that the photo shows the jets removed. I'm not 100 percent sure but I think the yellow arrow points to a plug which does not have any hole. It was two years ago since I did it so memory is not that fresh. I have a fully working set of carbs in the garage at home. I'll take the bowl off one tonight.
A blocked airfilter won't cause problems as described here, no harm fitting a K&N though!! A faulty HT lead, spark cap or plug can. The way you can rule this out is to move the sparkplugs (put 1 in 2, 2 in 3 etc) and see if the problem moves (feel the downpipes again). You can also swap the wiring on the coils. One coil fires cyl 1 and 4 and the other 2 and 3. Eg: There's no harm putting lead 2 on plug three and vise-versa. Just swap them over and again, see if the problem moves.