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Is it possible to change the analogue board and use the 74hc4067's for 64 inputs? Would it require additional programming? can the atmega handle all the inputs?

It can be done but 74hc4067 doesn't have an ESD and overvoltage tolerant alternative so you will have to use Schottky diodes on all inputs (64x2 = 128!). Also it doesn't seem to be as widely available as 4051.

would it take more programing on your part or do you think it would be kinda plug and play?

It won't take much programming but will require small changes to the Digital board. Also, only Atmega644 will be able to handle this number of inputs due to RAM limits on Atmega32/324. To be honest, I don't see much demand for this for now.