Put everything back together; start the bike and try to find that leak by spraying WD40 and/or water from a spray bottle onto all the areas of the carbs. You will be looking for a change in rpm's, and/or smoke coming out the exhaust. Spray around the boots, ducts, hoses, etc... You are trying to pin point the source of your air leak.
Download this manual: http://www.tocmanufacturing.com/File...nd%20Parts.pdf
The above manual will give you detailed easy step by step instructions for removing, disassembling, cleaning, etc. instructions for the carbs (Fuel System chapter 2). You will see that you don't have to take off the air box for this procedure; you need not be a mechanic.
As far as your second post above: yes. spray will hit the other ear if you aim from one to the other. Look at the air box as a big letter "T" whereas the top of the "T" would be the bike's ears, (spraying through one side will obviously hit the other ear) and the base of the "T" would feed the carbs & the emissions air valve, (see manual above). When reassembling the ears to the box, make sure all the pieces (especially the rubber ones) are snug/secured into place, thus preventing unwanted additional air to enter.
If your pipe, (I hope you mean exhaust) is burning up (color) this details a lean air/fuel mixture which can be cause by a couple of things; one being you do have a leak; extra air is going into that cylinder and you must have lots of popping upon decel.
Download that manual and read, read, read, especially chapter two. Ride safe.