well, it might cause it to run poorly for a little while, but I'd think the gas would clear out pretty quickly. You're saying it won't start with the filter in, but will run once its started if youput the filter back in? I'm confused by what you're saying here. please describe the problem more clearly.
If it runs well without the filter but poorly with it, then yes, its running rich. This may mean several things: you didn't really solve the problem, just made it a little better -- are you sure you got all the dirt out of the float needle?; you messed something else up in the process of cleaning the float bowls -- perhaps you've mis-aligned a float? float level can be pretty critical on some bikes.
If you can get it started with the filter in, what does it do when you rev it? Can you make some test runs to see if the problem is just at or near idle versus revving under load?