I'm not sure who Aku specifically is. Aku could be a person with a great imagination who tells all kinds of stories, like adventure stories, fairy tales or even true - life stories.
It could be someone from the Naruto universe who doesn't like Naruto's newfound fascination with Aku. For example, Danzo might see Naruto's interest in Aku as a threat to the stability of the village and try to stop Naruto from further exploring Aku - related things. So, Danzo could be the main antagonist in this case.
The character of Aku could be developed in a 'pregnant Aku in Samurai Jack fanfiction' by exploring how he interacts with the world around him differently. He may become more reclusive as he doesn't want others to see his 'weak' state. Or he could become more aggressive in trying to protect his pregnancy, which would be a new aspect of his character. Also, his relationship with his own power might change. Maybe he has to find new ways to use his magic that don't harm the unborn, which would force him to grow and adapt in ways he hasn't before.
Well, usually a funny Scotsman cartoon in JibJab might have exaggerated accents, traditional Scottish clothing used humorously, and maybe some comical stereotypes played for laughs.
One idea could be a crossover where Aku accidentally opens a portal to the Naruto universe. Naruto, being the curious and brave ninja he is, decides to explore Aku's world. They could start off as enemies, but gradually come to understand each other's motives and end up teaming up against a greater evil that threatens both of their worlds.
Well, without having the exact details of the 'Scotsman's Train Bedtime Story', I can imagine it might start with a Scotsman boarding a train. Maybe he's going to visit his family in another part of Scotland. As the train chugs along, he might be looking out of the window, reminiscing about old times. He could encounter a friendly stranger on the train who shares some local tales or secrets. And as the night falls and the train continues its journey, he slowly drifts off to sleep with the rhythmic sound of the train wheels on the tracks.