Maybe I'm not understanding correctly, but I'm having trouble reproducing your issues. (It's also possible things are also just behaving differently after the migration to 2.1).
- Cannot manually set a parameter as one of the added parameters (they only appear when checking the box)
I see all of the 36 parameters in the Unsorted tab when selecting a signal.
- When deploying a train schedule without setting the parameter, instead of the parameter it becomes whatever item/signal the parameter originally substituted (e.g. if you created the blueprint by substituting iron plates for parameter A, it puts iron plates on the schedule)
If I name a station [item=iron-plate], place a new train, add station [item=iron-plate] to the schedule, blueprint the train, set [item=iron-plate] as parameter A, and paste the blueprint with [item=inserter] as parameter A I see this reflected in the train schedule; the same behavior as with parameter 0.