I forgot to mention pneumatics for points, really low maintenance all of my line points (switches) have been powered by Air since I started using it back in around 2000. I have used Del Air, Easy Air (both now unavailable) and even have some Sunset Valley on my line though I find the Levers a little in the small size they do make a nice neat panel. All of my Lines go through modest sized Electrical Trunking, I spray it Grey to match in better on the line some I have even scored with a saw to look like Railway Cable Trunking runs. This for you will have the same benefits for me, easy access for revisions and perhaps some protection against critters. I have had ants nests in the trunking with no ill effects. The trunking is also useful for Electric Cable runs as I used to run DCC, but in your case with battery any such runs may just be for Building Lighting.
As for those water courses, embrace them use large rocks where they go to make like a River and run bridges over for the Track. I have made fake water courses on my line using Cement Based on top of Butyl Liner with the rocks bedded into the cement, so long as you preserve the natural route and depth of the water this should work well for you.