I'd try the filter without the lid on the box. If that cures the problem and the bike runs ok then it means there is a blockage somewhere in the intakes piping, somewhere before the air gets to the filter housing. If it runs rough when you put the filter back in without the lid it probably means the filter is dirty or over oiled. In that case I'd wash and oil the filter if it's a foam element, or replace it if it's a paper element. If you oil the filter use engine oil and give it plenty, then work the oil all through the element by squeezing it and working it in, and then squeeze it to get all the oil you can back out of it. If you wrap the oiled filter in a rag and squeeze it it works best. If you just use your bare hands to wring the oil out it keeps getting sucked back up off your hands, but if you use a rag the rag absorbs all the excess. If a clean or new filter still makes it run rough I'd check the breather hoses on the carby are not blocked and that they are on the right places. If all that checks out ok, then I think the carby needs some adjusting.. possibly just the float level. You could check that theory by turning the fuel tap off and running it and see if it starts to run right for a while before it runs out of fuel, which should take about two minutes if you are just sitting revving it. If it runs right for a bit, turn the fuel back on and try it.. it might have cleared the spark plug and excess fuel and it might be ok.. If not, you will need to pull the carby and clean it inside.