Sunroof delete question...

ok, im getting ready to yank the sob sunroof out...and that little drain "gutter" around it is rusted pretty bad on the front 2 corners....my question is would it be already to clean up the rust the best i can, and then put POR 15 on it all and go ahead and cover it up???

also if anyone has any tips on welding the top i would like to hear!!!

thanks
mike