Fuel issues

I have a 2003 350 Rancher ES. New top end, new fuel filter, fuel lines, and petcock. Also new carb. The problem is it will run till the fuel is empty from the fuel filter. Unplug fuel line at the carb and it will fill the line and filter back up. Once connected to the carb it will run fine till the filter is empty again. You can does this all day long. I can't figure out what's causing it to do this. Any help and thoughts will be appreciated!