Woah, why is the paint drying "all throughout the gun"? That should only happen if you disassemble the gun and don't clean it. Waterborne products are about the easiest thing to clean. Dump out the cup, flush water and/or soapy water through the cup and gun, then disassemble and clean out what remains inside the gun with warm soapy water. Reassemble and blow some air through it. It takes 5 or 10 minutes, start to finish.
I clean off the air cap and tip of the needle after each spray session, but only clean the gun at the end of the day. There's no need to unless you are spraying something that's catalyzed with a short pot life or the finish has something in it that settles out very quickly.
John