I don't think I'll be much help, because I hate sauerkraut, but here are a few thoughts.

- Is the sauerkraut in vinegar? I was thinking this might make the cream cheese curdle, but OTOH, I've made heated-up salsa (also vinegary/acidic) and cream cheese mixtures and it was fine. Maybe wait until the very end to melt in the cream cheese?

- I'd go ahead and add the mushrooms. They add some umami savouriness, and not too weird of a flavour on their own (IMO).

- If you don't want to use the jalapeno, you can chop it up and freeze it. They freeze quite well just like that, no need to blanche or anything like that.

Hope it turns out.