Unfortunately I don't understand most of the discussion in this thread.
OPA350 has already typical input current of 500 fA, 10 pA maximum. It will work for pH measurement with standard requirements. You can use OPA129 for guaranteed fA input current. Consider that a unsuitable circuit layout and processing can easily cause much higher leakage currents. Advantage of OPA129 is that the pin layout supports a guard ring design, review the datasheet for layout suggestions.
It's not clear in which regard your level shifter circuit is "not working". The shown circuit can't work in reality because OPA350 voltage supply is limited to 5V. Maybe Proteus knows about OPA350 supply voltage range. You can e.g. use OPA350 with lower supply voltage for the input stage and OPs with higher supply voltage for the remaining circuit. OPA129 is designed for +/-5 to +/-15 V supply.