I looked at the exploding drawing on bike bandit for the carbs:
The front and rear intake manifold boots are different part numbers.
The hose clamps that hold the carb bottom onto the tubes comes off, so if you left the original clamps on the original boots, they would have been pointed in the right direction if the boots were put in the right location.
If you had taken the clamps off and got the boots mixed up, all you had to do was spin the clamp around and unscrew it from itself, flip it over and put it back on. Easier typed than done - I know.
Since you have the original boots back on, if you can see the part number molded into the boots, you can tell if you have them in the right place, and go from there
but if you have everything fastened down and the air filter intake side is all connected and nothing is strained, I dont see a problem if the carbs are slightly tilted to one side. If the bike is running ok I would let it go till the next time you check the valve timing (another 12 to 16k miles maybe?) and then swap them back when you have the carbs off. To quote the first rule of motorcycle maintenance: If it aint broke, dont "Eff" with it.
The last time I had the carbs off my 650 for a valve setting check I did not notice that the carbs seemed to be tilted. I think I would have noticed it if they were, but cant be 100% sure. I had a hard time getting the clamps on the top side of the carbs back on to hold the airbox in place - took me three attempts to get the air box to stay seated while I tightened up both clamps - about 30 minutes.