Valley pan or 'turkey-tray' gasket was designed to keep hot oil off the base of the intake manifold where the exhaust gasses are routed thru for quick warm-up. This area gets hot enough to char the oil after a while. If you have blocked off the exhaust crossover, or run an aluminum intake, or change your oil regularly, you don't need the pan. But by trimming off the intake port section of an old pan with scissors, the bottom part can be laid in position and better composition gaskets used to seal the intake ports.
As for the rear side windows, what do you want to do with this area? Main airflow is up from the bottom of the car and out the rear opening, so adding side scoops does nothing except add drag, unless flex-tubes are connected to the scoops and led to a box around the air cleaner. There are two side-scoops available- a small and a large. Silver State runners have proven that the small one is cosmetic only- airflow along the body stands off about 2" so zero air is 'scooped'. The large ones, also called 'elephant-ears,' do protrude far enough to scoop air. But the window frame they fasten to is only held in the body by friction so when it starts to work (at around 150mph), the scoop may tear out of the body unless the frame is rivited or screwed in firmly. Expect some high speed carb-jetting problems if you do get the big scoops to work.
