I am concerned that you do not have NuPIC installed correctly. How did you install it? Did you compile it yourself?
You combine different encoders using a MultiEncoder. This simply concatenates the encoders.
I don’t think you can do this. The anomaly indication represents the complete state of the system.
Try some different values for TM parameters here:
https://github.com/numenta/nupic/blob/master/src/nupic/research/temporal_memory.py#L82-L86
Increasing the permanenceIncrement
should make the TM learn faster. Increasing the permanenceDecrement
will make it forget faster.