I would start by looking at the rides and determine which ones you want to ride the most. That will really influence where to "start" and how to proceed. Disneyland is not that large, so you can afford to criss-cross the park without losing to much time (especially for rides near the entrance to each land).
1. Do you want to ride thrill rides (e.g., Indy Jones, Space Mountain, Matterhorn, Star Tours, Big Thunder)? If "yes", then these are probably the best to get fast passes for, if available and/or applicable. I would probably FP Indy and Space. Big Thunder doesn't always have their machines on, there iso FP for Matterhorn, and Star Tours isn't high on my list (so a personal preference).
2. Do you mind getting wet (e.g., Splash Mountain)? If "yes" then consider a FP for this. Just remember, you will get wet (maybe soaked), so you'll wet for a while afterwards. I might save this for the very end, except you'd be cold.
3. Do you want to ride the kids' rides (e.g., most of Fantasyland)? Again, these are better later in the day (except Peter Pan) when the little kids have gone home. You can often get in Snow White, Pinocchio, and Mr. Toad in, in less than 30 minutes at the end of the day. Peter Pan always seems busy.
4. Do you want to ride the "classics" (e.g., Jungle Cruise, Pirates, Haunted Mansion, Small World)? Luckily, these can fit it in pretty well throughout the day.
Given you only have one day, I would opt for counter service meals.
Regarding the shows, it's a balancing act. While the shows run, some the lines for some things are shorter. I love the fireworks, but it will eat into park/ride time. For Fantasmic! you have to decide how close to the front you want to be. If you're willing to have a partially blocked view, then you can wait to get your spot until closer to show time. If you want to be in the front, then you have to plan on being at your spot 2 or more hours before the show.
I haven't found the Disney Mobile Magic app that helpful, but I'm not a Verizon customer (it was originally designed exclusively for Verizon). I've used MouseWaits California and DL Waits. Neither were always accurate, nor did one seem consistent better than the other. I used them to give me a ball park figure of what was going on at various rides.