Use a byte-coded solution.

Start with some global configration bytes informing about inputs and outputs etc.

Then transfer an array of bytes, where the bytes represents commands and each command can take optional bytes for parameters.

Take 8 pins to be arbitrary inputs or outputs
Take one byte internally as 8 virtual state cells
Take 8 bytes internally as 8-bit counters/accumulators

Send configuration, telling which pins you expect to be inputs and outputs. Possibly configuring delay timers etc.

Send array of commands.

Let the program continuously loop through the byte-coded commands, performing calculations and producing results.

By adding new byte-coded commands, you can make the processing as complex as you like.