what is the best way to weld this and with what machine? also would a mild steel flange of a stainless steel flange be better for this? thanks

 

All you need to do is strip the coating off ~1" from the weld. Otherwise the burning gas is a bit toxic. Once its stripped, its just mild steel. Any cheap MIG will work on it. A mild steel flange will be best, as you usually only get surface rust on a 1/2" slab of steel. The vast majority of stainless manifolds come with mild steel flanges.