Let me try to summarise. If you do not disturb anything else, but you put the lid on the air filter box, it won't start. This applies whether or not there is a filter element in the box. However if you remove the lid, it will start, whether or not there is a filter element present. Please confirm that this is correct.
If that is correct, I think the next thing to try, is putting the lid on the box but not screwing it down: push it down into place, but do not put the nut on the top. If it still doesn't start, lift the lid about 1 mm and let it sit there, still without the nut, and try again. (This is aimed at seeing whether the problem is distortion caused by the clamping nut on the top of the box.)
