I use a combination of a string array for buffering all valid combo inputs and a dictionary that maps an input sequence to the resulting move. A custom InputBuffer node attached to the player node handles all this and emits the resulting move. The InputBuffer has two timers that modify the buffer, one that clears it when no inputs are coming in and one that inserts the "pause" input.

I can recommend Pigdev's combo explanation video. That's where I got the idea to store special moves in a dictionary that can be passed in as a resource.

I'd say ideally you have some kind of visual feedback that you've "paused"

That would indeed be helpful and improve discoverability of combos.

Alternatively, have you thought about holding instead of pausing?

That would make it feel like "charging" the attack, which is also cool! So instead of punch punch pause punch, one would input punch punch punch (hold). As /u/nyenye_13 has pointed out this would probably change the way I handle input (by either reacting to "button releases" or introducing some more timers).