I'm not sure if this will work for you but on my 1100 I took out the 4 bolts holding the battery box allowing it to move back a bit. The I installed the air box, without bolting it in, with the boots attached. When putting the carbs back in I rotated the carb rack so the carbs were pretty much facing down. Slid the carbs in with the back sides, the sides that go to the boots, facing up. Slid them in and put the front of the carbs down into the carb holders and used a screwdriver to get the boots up over the bottom half of the carbs. Once in that position I was able to completely push the carbs into the carb holders. Use a lot of silicon or Vaseline to lube up the inside of the carb holders. Vaseline is not needed and not wanted on the back of the carbs where they go into the boots. Once carbs were fully seated into the carb holders, and clamps tightened, I was able to maneuver the air box so all 4 boots slipped onto the carbs and pushed the spring looking clamps onto the carbs. Only then did I start bolting the air box and battery box back down.
Hope that helps. Al of these bikes seem to take different techniques to get them up but one thing that is common is to put the carbs into the holders first then attach the boots. On some bikes instead of having the carbs inserted above the carb holders and boots, you go from underneath and work them up into the holders. It just depends on where your bike has more clearance.