Hi Val, Wish I remembered how to quote from your post, but I'll try to answer each question.
1 It is great for a throat to stub ended tracks. You want to use handthrows, right? The Pecos do a good job of routing power with their clips in indents on the throwbar. Sounds like the electro frog turnouts route as they come, so you could use them with no additional feeds and no gaps and not have a problem, as long as all those railjoints never allow bad contact and voltage drop becomes an issue. If a joint becomes a problem, you can gap and add leads as required. If that's something you want to possibly deal with later. It would probably be fine to go ahead and solder all your rail joiners. Some don't like that. Adding leads later is often no problem, depending on access. Determining where to add gaps is easy. Perhaps someone will post a diagram or link to one. But here is how you figure it out. Oh, and I answer your next question.
2 A short is a connection of opposite polarities with little to no resistance. Since both rails of a diverging route are the same polarity, there is no short. There is no complete circuit. So, if you look at a drawing of a ladder with the track coming in from the left and the throat extending to the right, and the top rail is marked positive and the bottom negative, you can follow the positive and negative routes. When you get to a frog, remember that all rail connected to that frog will become whatever polarity you have connected the points to. So one route will be live, the other dead, for its entire length. You then reach the next set of points and the process repeats. If you have to add a feed ( and lots of times cleaning and soldering an offending railjoiner is all it takes) do so wherever needed, and gap just before it. Connect the feeder to the appropriate bus. Just remember north rail always white, south rail always black, or whatever color you use. The trackage above the gap will no longer control the polarity of the trackage below it. So, depending on where the new feed is, another track will stay powered, defeating your signalling scheme, but otherwise will work well.
Actually, I think I've answered the other questions too. Hope it was clear enough to make sense of. A drawing would be good!