Depends on if you run with the fringe on your bike. I have not had any problems with mine, I used to carry the football to put it on when it rained, but have not done that this year, and have had no problems. After a big down pour I went out to leave & it fired right up, no stumble, so I quit worrying about it.
i have the hd cover on mine and it fits like (EDIT) , but im still running it as kind of a prefilter to cut down on so dirt befor it gets to the filter.