I forgot to mention what a pain in the ^$$ those two bolts can be to get in and out.
I used a long extension with a swivel on the socket end.
I wrote this in answer to another person having difficulties in getting his airbox aligned.
He already had the carbs off the bike.
You may need to start from scratch.
You
may be able to get away with loosening the clamps on the head to carb boots and twisting them to positions where your airbox will align with your filter housing.
I am doubtful it will be that easy.
Chances are that the carb to airbox boots are not sitting on the carbs flush as they should be.
Take note as to the order of attachment.
What you need to do is attach the airbox to carb boots first.
After that you twist in the head to carb boots.
This is what I do to get the carbs/airbox/filter housing in the correct placement.
Remove the filter housing.
Loosen the airbox to frame bolts to where they will just hold in the airbox. (this will give you a bit of room to slide airbox around without the agrivation of trying to get the bolts back in when everything else is proper and tight)
Use a object to hold the carbs up level to bike for attaching the choke and throttle cables. (the right side works best and you want your carb stand high enough to hold the carbs up with cables attached so you can take a breather without having to hang the carbs off the cables)
Attach the choke and carb cables being sure the carbs will insert into airbox without twisting the cables.
Slide carbs into correct area while insuring the clutch cable is gently positioned into bracket on side of carbs for it. (the clutch cable will hang them up otherwise)
Slide carbs onto airbox boots and tighten clamps while making sure the boots are positioned correctly on carbs.
(I am sure many peoples airboxes are warped around the boot area and after attaching to carbs correctly you can use some heat to let the carbs pull it back into shape)
Boots at head.
Start with the two innermost boots and push smallest area of boot into largest gap between carbs and head and twist back and forth to seat them.
Temporarily reattach the filter housing to the airbox and position the two seated boots by twisting them to level out and correctly position the filter housing.
Remove the filter housing again.
Mark the top center on the two boots with a paint marker or a piece of tape.( They will be offset from each other,make sure the area is clean first and the paint drys well before next stage)
Put the two remaining boots on using the same method. (the marks on the other boots are in case you have to move them to get the two outside boots into position)
Make sure the boots are all seated correctly and not causing each other to bind at all.
Tighten clamps. (be sure to position screws on clamps to where they will not interact with the throttle or choke)
Tighten the airbox to frame bolts.
I clean and mark my head to carb boots before I remove them so less trouble the next time.
Tried to take a few picts as how my front boots are twisted to give you a idea of how they will look.
You will see that mine are marked with cylinder number and a line at the top to align them. (looks like my mark is off a bit on a couple)
If you get them on correct I would recommend doing this after in case they ever need to be taken off again.
This last photo is with my bike on a lift.
I am pretty sure the rear tire is in a raised position (its off so I cannot confirm that)
You may need to print and compare angles with your head to observe the level you will want.
Hope this helps.