Eric,
The "Phase" you use determines what era your modeling. The latest is Phase V, which is sometimes referred to as Phase IVb by some modelers and manufacturers. If your trying to model the modern day, this is the phase you want. If your shooting for late 90s, early 2000s, Phase IV. Kato made some superliners in Phase III to go with its F40PHs it released a few years ago. Walthers produced alot of Phase II Amfleet cars over the years. The Phase V/IVb cars are harder to find. In fact, I believe only Bachmann made the Phase V (IVb) Amfleet cars.
I also think that only Walthers made the Phase IV and IVb Superliner I/II cars. They are very sharp, with polished aluminum finish and while MRSP is like $53, you can find them for $35. I dont have any of them right now, but they are on my wishlist for one day. The major difference between a Walthers Phase IV Superliner coach and a IVb coach is the "Amtrak" logo is by the door on the Phase IVb. There are some minor differences between the Superliner I and II cars on the prototype like its disabled-person friendly and the door is a little different, etc.
Also, both in the prototype and in HO modeling, only some Phase IV cars are available and are run. For example, I have yet to see a Phase V or IVb baggage car in prototype or HO, and what is out there, is somewhat hard to find. Good news for you though, is that the Phase IV/IVb Superliner Baggage cars(which youve already acquired) are available.
It looks to me like your heading down the right path. Enjoy!
Brad