The diodes will have no effect unless the voltages go above or below VCC. They are there for input protection for the Arduino.
I'm still a bit confused and don't have time to read the whole post again, but it looks like your voltage divider resistors are far too small. I would use something in the 10k to 100K range, but same ratio. That's the values for R1 and R2. Simply multiply each by about 100 to get values that will not load down the circuit.