you can use a filter and that will help some. but i think that Jegs or someone sells a small grill that you can insert into the scoop. not sure ifit will fit the factory scoop on the car, but worse comes to worse, i dont think it would be hard to build one.
you could get a piece of metal and weld it infront of the filter (if your using the stock base) about 6 inches in length. Get a K&N filter, water wont hurt it as much as a paper filter. If you drive in rain soaked country, fasten cheesecloth under the scoop and take it off if you show it, a screen will still allow water to go thru.
The ram air system is basically an aircleaner lid and filter within a larger base and a rubber seal. The air (or rain) goes through the scoop and air inlet, hits the inner lid and is diverted around to the sides and into the filter and into the carb.
In the Cougar/Cyclone/Cobra/Torino 428CJs the 14" inner lid and low profile filter is the same size as the 289 HIPO that fits inside a larger base. The Mustang 428CJ and 351 Shakers have a drain tube because water can collect at the shaker base. I think that water that collects in a Cougar non-Shaker base will evaporate from engine heat and/or there is enough of a trough for it.
Also Royce P had some information about the K&N Xtreme fliter top, basically it doesn't work too well and actually hurts performance. Too much unmanaged air is not good. You're better off with a solid inner aircleaner lid. The Xtreme wouldn't be good in the rain anyway.
I don't think the flapper is necessary for a basic ram air system, but some sort of a seal is.