You're absolutely correct on the basics. And, to your more advanced questions:
1. Yep, it never goes back up.
2. Um... hmm, that is very hard to answer, because it varies by AI type, by random map seed, and other factors. The train master obviously has a ton, something like 80 on an 80 planet map is likely. For everything else... again, it's going to vary, but if I had to guess I'd say it would be around 20-40 on average. If you turn on a game with no Fog of War, you can easily count. There is one train per train station. And, with the train masters it is two trains per train station, and they get more stations.
3. Nothing reduces the number of trains aside from actually killing them. On lower difficulties, those trains can be "stranded" without a way to move out of territory because they aren't allowed to go through your planets, though. But otherwise, they just become denser on the remaining paths.
4. For trains, they generally prefer to path to a planet that is about 3 hops away, or 2 if not available, or otherwise just whatever. But inside that, it's intentionally completely random.
5. There are only marks I-III, and those are completely determined by the difficulty of the AI you select. On easier difficulties you get the MkI, on the standard ones you get MkII, and on the higher ones (9/10 only, I think) you get MkIII. They all behave absolutely identically, but have weaker/stronger stats depending on their mark level. Per AI player, you'll never see a mix of the mark levels in a single game (but if you have a very high level AI, and a very low level AI, you'd then see different levels between the two players).
Good questions!
