Welcome to the RTA Forum - and thanks for doing your homework before asking your question!

It seems like you actually have a very good grasp of things, and I don't think these responses will be at all a surprise to you.

First, going down the coast first is probably your better bet, for the exact reason you talked about being closer to the ocean and you won't have to cross traffic to get into the turnouts. There is nothing wrong with going south to north, in fact that's how I've done the trip and I really don't feel like I missed anything, but if this is a loop, I'd go north to south along the coast since that's the one area where you could notice a difference in the direction you choose to travel.

For time of year, I'd choose the fall. The Sierra Passes will be beautiful any time you travel them (and in September, you should start seeing some fall colors too!) but when you factor in the major detour that's involved if the passes are still closed in May/June, I'd go later. Again - if you could only do the trip in May/June, I wouldn't let that stop you from doing it, but if your options are equal, I'd go in September.