The question I have is does anyone recommend a particular configuration of the I/Os so they are safe from the extremely harsh environment on both aspects: electrical and mechanical / chemical (vibrations, water and (or) other fluids).
Potting the PCB with epoxy products will solve the mechanical and chemical problems, as far as the electrical isolation is concerned, use optocouplers TLP504 for digital I/O and HCNR200 for all your analog staff.

Al.