Ryan, I would advise against any kind of "race the clock" scenario. That's going to lead to very fast running and probably some spectacular wrecks (unless that's what you're looking for.) Personally I'm going to avoid it.
Your "Mode 2" is the most similar to my board game. Each passenger (a penny nail) is painted one of four theme colors which correspond to the four stations on my board. Once picked up, a passenger can only be delivered to a station of the corresponding color for points. Monopoly dollars are awarded to keep track of points for both passengers and bonus segments.
My prototype gameboard has a pre-existing, fixed track configuration which is used by all players, and provides a persistent visual representation of the game state. Players take turns moving their "RDCs" (bits of wood with a magnet on the bottom) around the track route network to pick up and deliver passengers. Since my game is turn-based, I introduced a "red block" rule. Basically a player can't move into a track segment if doing so would create an unavoidable head-on collision with another train. In my game the trains only run forward. This is unrealistic, but it makes the game more interesting.
For purposes of the game, I defined a "segment" as all of the track between any two switches. Segment length can be anywhere from 10" to 10 feet. Your idea about the flashing LEDs to indicate a bonus or required route is exactly what I was thinking, although in the real world, you might need a lot of LEDs! Only one sensor would be needed anywhere within a segment to confirm that a player's train crossed it.
I live in the Fort Worth medical district and have many friends who work in health professions. My layout will be on the ground floor of my home, just inside the front door. The room is tight, but if the concept creates joy on a small-scale, maybe I could get buy-in to build something larger off-premises. I also hope to host young adults with autism, scout groups, and especially my friends! So many people haven't been properly exposed to our hobby. Hands-off round-and-round running like I used to do at train shows doesn't win many converts IMO.
Because CAB-2s are pricey and now discontinued, I was planning to run trains with CAB-1Ls. I'm still working out how I can integrate freight into my model economy. I would love to include physical operating accessories too, like the magnetic crane, culvert loader, barrel loader, cattle pen, etc. Perhaps not strictly realistic, but they are fun and interactive, even if they don't work perfectly every time. I want what I build to foster interaction with the machines but especially between operators. Also, variety, and imagination.
