I had an air filter that had deformed so just wouldn't sit into the channels correctly and airbox lid wouldn't fit. Filter should just slot in nicely, that's worth checking.
You say the top won't go back on, but then say everything has moved left....There's no point trying to put the top on if the bottom section isn't in place. I wonder have you missed the pipes on the underside of the airbox and now they aren't letting it seat correctly. Were you able to screw in the velocity stacks?
Thanks....I had to take it all apart and re-seat the throttle bodies...boy they were a PITA, I used a bottle jack(with a 2x4 up to my floor joists) to press them down....
Now I have a code after starting
Its ait temp sensor (9 short flashes of the fi light )
That fault inidcates that the lead to the IAT is probably unplugged, it is in right the bottom of the airbox on the 5th gen. It is a white sensor with a fine wire.
I never had much difficulty with throttle body boots, I have used a smear of silicone grease on them to make them slip in easier, after that just a firm press down will seat them, as long as the clamps aren't too tight below...warming them with a hair dryer can also make them more pliable.
Before you go digging into the airbox again, you can try clearing the MIL fault indicator. You may have trigered the fault if you switched the ignition on with the IAT disconnected during the rebuild.