if its a paper element filter. like pictured, replace it. if its a screen, sponge, fiber, cloth etc filter google search what you have and look for instructions to that particular material. Simple green is water based, so not as good of an idea. but better than nothing if you are getting all the dirt out.

are you saying there is no airbox? like the previous owner made a short ram intake of sorts? it will be ok, but extending that into the wheel well would improve performance.

i would cover the alternator, intake and battery/fuse blocks.. those are areas i wouldnt ant soaked with water.