i agree with warren. you're better off drifting around casting flies covering water than trolling. you'll learn more and actually be fly fishing. learning the water types is key, and success trolling in an area doesn't always translate into success fly fishing.
tie up some chartreuse and white flashtail clousers and half and halfs. grab a 300-350 grain line (i prefer the rio striper lines) and go at it. using the right lines and using a water load to cast them makes casting clousers easy and safe. to me, shooting head lines are the only way to fish out at neah bay. you'll save time and energy over full length lines (and they are safer to cast in the wind imo).
as for time of day, look at a current book. maximum ebbs and floods will usually translate into the best fishing for me. hard currents also make light levels less important when it comes to the depth the fish will be feeding. for me, the topwater fishing is less about low light, but more about finding the right current, bait, or situation to fish them.
unfortunetely for small boats, and as warren mentioned it's been lumpy lately,
the best fishing is indeed around the currents... and currents (especially ebbs) make rough water rougher. be cautious on an ebb, especially near the entrance. floods offer some of the best fishing, and the current flowing in usually flattens the water.
but the fishing has been top notch. the fish are bigger than i've ever seen this early (and not just a few, but the average is high). today we landed 52 coho.