Detect electrical signals from plants
If 3000 samples per second are needed, I would suggest the data logger to be build on some ATMega with built-in DAC and several analog channels. Through the UART this setting will be connected to a simple PC.

The hard part is to build the mV precise amplifier for the ion probes. This amplifier has to be very high impedance, with high gain and probably with differential input. But there are cheap and precise opamps these days, so it is not a big problem IMHO. At least $100 should be more than enough. 

I can't point you to exact reference for this analog part of the project, but I have some memory that I saw something similar in the great book "The Art of electronics". Search there for some schematics.