so I can't use a single 4051 multiplexer
You can run one multiplexer on each analogue input, this shows two being used but you get the idea:-
http://www.thebox.myzen.co.uk/Hardware/MIDI_Footsteps.html
However, the more you have the longer it takes to get round them all. It is not so much the switching time but the settling time. If you have enough to trigger a logic input you could put a port expander on the SPI bus the MCP23S17 is typical. This would have 16 inputs and could be set to trigger an interrupt when any input changes state. The interrupt service routine then gets the data from the chip to see which input changed. You can have up to 8 of these chips on the SPI bus without any further work.