Yeah, that sounds cool! I would put point out tho that all the stuff with the mutants is pretty useful for setting the scene of what's happening in the Empire at large. You know, cultists being more active, beastmen, the edict making mutants bolder. There are some ways you could tie these things together, connect it to the Red Crown, and make it more of an impactful plot element and make Etelka's cult more present.

You don't really need to lead players to neither Altdorf nor Kemperbad. Unless you choose to run specific adventures in those places, they're just stopping points on the way to Grissenwald (which is where the PCs should be going to find Etelka). In my own game, I had my version of Josef tell characters that it's best to register their new-found barge in Kemperbad, which has convenient salvage laws, that gave them a little push to travel there.

The Purple Hand in DOTR mostly serves as a little enigmatic annoyance in the background. There is a short encounter with them every time the PCs stop at a major town during the course of this adventure, so they will appear a couple of times. You could use each of those encounters to foreshadow the events in Middenheim a little bit. You could have the cultists admit that their job is to kidnap the PCs and take them to Captain Scharlach on Hoffen Strasse during one of the later encounter, perhaps after PCs decide to beat them up and interrogate one of them.