Lets see if I can help answer a few of these questions, but please keep in mind I am in a different location then you (Maine) and our weather is quite different. Still I think the same principals apply mostly.
First with run-off plumbing. The standard drop per foot is a quarter of an inch. That is for every foot of horizontal run, you drop your pipe down by a quarter of an inch vertically. Incidentally, this is the ideal slope. Dropping your pipe more per inch does NOT make for a better drain, it actually makes it worse. The reason is, with a 1/4 inch slope per foot, the water is moving enough to help carry any solids along with it. With a steeper pitch, the water runs out leaving the solids behind. You should not have many solids in your case, but leaves, grit off the existing roof, etc may get into the pipe so staying with the 1/4 pitch drain makes sense. By the way, an easy way to get the proper pitch is to take a block of wood that is 1' thick and tape it to the end of your four foot level...whallla...when the level reads level, you have achieved the 1/4 inch pitch.
I am not sure rolled roofing is the way to roof a flat roof. Now I am from Maine so flat roofs are unheard of here. Still I can picture what you are doing and I think if you can not be persuaded to use rubber roofing then you may be in luck. Here in Maine we use Grace Ice and Watershield a lot. I have used it on my eves and on my valleys for added protection against leaks to my over-laid asphalt shingles. I even use it around my windows and doors as a sort of flashing. In fact, on anything less than a 5/12 pitch, we use Ice and Water Shield up here on the whole roof.
Its neat stuff. It has a very sticky backside that is covered with plastic. You peel this off and stick it to the roof. Then on the next coarse you overlay it by 6 inches and go again. DO NOT let the stuff touch itself. It is so sticky that it will not come off. Just cut it and start over.
The stuff is truly incredible. What happens is, as the sun warms it, it turns it into this thick layer of roofing tar that seeps into nail holes and makes the roof water tight. We use it on the eves because in the winter the freezing and thawing of snow will back the water up under the shingles. This Grace Ice and Water Shield is so waterproof, it stops that. Its expensive though. 150 bucks a roll. Still I think if you laid this under your rolled roofing, you would be alright. I would still rather see you go with a rubber roof, but this is an option.
As for the 4 x 4's, I really cannot say. I am neither an architect or a structural engineer. Considering you have no snow load out in California, nor any live loads above it, it sounds like it would hold, but that is a very bad assumption to make. Better find out from a more qualified individual than me.
Hope all my typing helped you...
I have no intention of traveling from birth to the grave in a manicured and well preserved body; but rather I will skid in sideways, totally beat up, completely worn out, utterly exhausted and jump off my tractor and loudly yell, "Wow, this is what it took to feed a nation!"