Ray, a suggestion that might elicit more response would be to start a new thread not using MTH ITAD in title...or since you started this thread to modify its title with keywords like RF ID or whatever. That is, I think you confirmed your occupancy detection application has been resolved (for now that is!) and we're now talking about identification.
As I muse about it, it might be useful to separate the occupancy issue from the identification issue. While one might imagine using a common technology, I think it depends on what you need the ID info for? Obviously if you only tag the engine you can't use it for occupancy detection to close crossing gates or whatever. Even if you tagged every piece of rolling stock if your detection range is just a few inches, a long freight or passenger car or just about any engine would require multiple tags or else a stopped consist would not be detectable.
When you first posted about detecting the GG1 vs. another engine, I took the very narrow interpretation that you wanted to know if its the GG1 or something else. To that end I can imagine a limited application where you simply place a 10 cent magnet on the GG1 and a 25 cent reed switch or solid-state Hall sensor on the trackbed. Then if tomorrow you want the GP9 to be the "featured" engine, then you just move the magnet to the GP9 and now it will trip the detector that causes activates certain layout functions or whatever. Or if the application is to just have steam-engines trip some action related to, say, a water tower or coal tender accessory, then the magnets would just go on steamers and not on diesels. Etc. Etc. In other words it gets back to exactly what you are trying to do - not telling you anything new but wondering if by carefully sorting out the must-haves from nice-to-haves that perhaps there's a simple solution we haven't thought of! 
As for the CV application, my first thought was how on earth are you going to detect the different between different GP9's that only differ by engine number? Sure, you could write software that first detects it's a GP9 then knows where to look on the cab for the engine number to then run character recognition software but really?!
As for LCS, I think you've ruled it out because its an active system requiring power on the engine side not to mention finding space to install it. But since you say you're up on "PIC" like technology, it seems you could roll-your-own transponders blasting continuous unique ID patterns out an IR LED pointing at the track. Using a 6-pin 50 cent SMT PIC with a SMT IR LED on a 1/32" PCB from OSH Park would be just a few bucks each and might be easily mounted under any engine running 2 power wires up into the engine to get 5V DC power. Don't need the fancy LCS track detectors - just use an IR phototransistor and let the Arduino decode the passing bit patterns. Yes, there's some homework to be done but we're just talking! 
