If you are using all of your PCI slots, including one for the slot fan, then you don't have to worry about perforated PCI slot covers as you obviously don't have any. Your arrangement is optimum for use of a PCI slot fan in a MDD G4 (i.e., in the slot next to the AGP video card) even though the fan is pulling hot air from the back side of the video card. Ideally, one would want to pull are from the front/VPU side of the video card, but that is usually not possible because of the MDD G4's physical configuration.
I don't think I fully understand what you are asking regarding redirecting your medium size case fan. In general, one should attempt to move air in a MDD case from the front and sides to the rear. Also, remember basic fan laws (i.e., fans in series increase pressure, not flow volume (cfm), and fans in parallel or just a bigger fan increases flow volume, not pressure). Usually you want to increase volume, but in a highly restricted exhaust environment, you may need to increase pressure in order to get the fan moving air volume at its designed flow rate.
Carl B.