Okay, we have several things going on here.
First of all, you do need service pack 2 (I think it is), which added passenger train options to TRS2004. Without that, I have no idea what all will happen.
As mentioned in this thread, it does help to delete the cache file (/cache/world_cache_dispatcher.chump) when you add new components.
There is a thread in the TRS2006 forum named Monorail Information that includes the link to the site where you can download the Release Notes, which can be useful in tracking KUID numbers. If you have read the FAQ, than you probably already have the notes, which is a good thing.
I believe there are 119 items on the DLS, so you may still be missing a couple of things. If it is something that objects (for example the train vehicles) are dependent on, those objects generally will not show up, or will display unpredictable side effects. All the KUID numbers are listed in the Release Notes, so you should be able to check the numbers you have against the master list in the notes.
The junction controller rule is available on the DLS.
I have uplaoded a number of improvemnts (bug fixes, texture improvements etc.) to the DLS, and that is the only place where all the current content is available. Sorry if you're having trouble using it, but that's really the only place to get it.
I hope this helps straighten a few things out, and I'll try to monitor this thread a bit closer for awhile.
In the meantime, I can no longer download directly into TRS2004 because the TRS2006 components grab the session and install everything into 06. If someone could post a message in the Monorail Information thread in the TRS2006 forum and write up the steps for downloading for TRS2004, I would appreciate it.
JFE.