MIDI is much simpler than Linux – you may be over complicating things in your mind.
One thing I don't understand is: how does the pedal know the Timefactor is there?
It probably doesn't (no need – it's job is to transmit). The TF will know that the pedal is there when it receives something.
The pedal changes patches on the timefactor out of the box, which is pretty cool but that seems to be all it does
There are essentially two type of MIDI controller (pedal). One type just sends a Program Change message – this would appear to be what you have. The other type is a "Constant Controller" or CC, which is used to change values (e.g. knob settings). Yours may well not be able to do this – you should study its manual.
MIDI messages may be sent on one of 16 different channels – each receiver will listen on one channel only, so that it only gets the messages that it is supposed to. The exception is OMNI, which means that it will respond to messages on all channels.
Most of your other issues seem related to expecting MIDI to be more sophisticated than it is. It is just a simple send and receive system, not any kind of network. Typically a sender does not know if anything is receiving its messages. So, no automatic sensing or other fancy stuff.
My guess is that you probably need a better pedal which can send CC messages (see above) – then you will be able to control TF parameters.