Fishing from shore - I always start after low tide and fish the incoming tide. Time of day doesn't really matter.
Fishing from boat - Slack tides (1st qtr moon or last qtr moon). Full or new moon? Hardly worth it, requires a lot of planning and the weather to cooperate because the window between coming full high tide and then going slack is very narrow, maybe an hour at best and then the current gets so strong you can't keep on the bottom or your drift speed is too fast.
Bait - Depends on the time of year. Cooler months, there are often mackerels feeding right outside the harbor, just watch the birds. Same at Cholla just outside the bay. Use a sabiki rig. drift (or motor south a bit) in 30-40 ft of water. Small sand bass will hit the sabiki over rocky spots and are great for grouper. Gets sandy out in front of Manny's and you can catch a lot of bonefish. These are the BEST grouper bait and are tough and hold up in the livewell. I have some marks for a couple of bait reefs about 10 miles out. Again, sabikis. Can usually get macks and sardines during cooler weather. But put the sardines in a bucket with ice, not the bait tank. They don't live anyway and will just foul up the bait tank for anything else you have in there. Warm weather will get you nothing but lizardfish (worthless) unless you're right on the reef. You'll get sand bass here, too, but they don't hold up in the bait tank because the water is deeper and they decompress. You're better off catching sand bass closer into shore where it's shallow. Sometimes, you spend more time trying to make bait than it's worth. Always take squid with you as a back up. Everything eats squid. Shawno is a jigging fool but he catches some nice fish that way. We'll jig or use extra large swimbaits on a lead head for shallower fishing, but on the deep reefs, we go with a multiple hook setup with baitfish and/or squid. Jigging in the heat will wear you out in a hurry!
Trolling is a whole different story.
Joe - I'd be willing to guide for you a time or two. We'll see.