Ground Wire (or Wires) after PEX Installation
Run a new wire from the panel to the 2nd metal rod, and to the water main coming in

You'll want to run a new copper wire (minimum size 6 AWG unless your service is upwards of 200A) from the panel to the 2nd metal rod, and also run more of that copper wire from the panel to the water main coming in.  That way, the water main itself is bonded to the electrical system, and all ground electrodes present are tied in (it's actually against the NEC to have a ground electrode, other than a buried concrete-encased electrode, that's not tied into the mains grounding system).

See NEC 250.64(C) for what prohibits you from splicing to the existing conductor attached to the 2nd ground rod:


  (C) Continuous. Except as provided in 250.30(A)(5) and
  (A)(6), 250.30(B)(l), and 250.68(C), grounding electrode
  conductor(s) shall be installed in one continuous length
  without a splice or joint. If necessary, splices or connections shall be made as permitted in (1) through (4):
  
  (1) Splicing of the wire-type grounding electrode conductor shall be permitted only by irreversible compression-type connectors listed as grounding and bonding equipment or by the exothermic welding process.
  
  (2) Sections of busbars shall be permitted to be connected
  together to form a grounding electrode conductor.
  
  (3) Bolted, riveted, or welded connections of structural
  metal frames of buildings or structures.
  
  (4) Threaded, welded, brazed, soldered or bolted-flange
  connections of metal water piping.


and NEC 250.50 for the requirement to use all available electrodes for grounding:


  250.50 Grounding Electrode System. All grounding electrodes as described in 250.52(A)(1) through (A)(7) that are
  present at each building or structure served shall be bonded
  together to form the grounding electrode system. Where
  none of these grounding electrodes exist, one or more of
  the grounding electrodes specified in 250.52(A)(4) through
  (A)(8) shall be installed and used.
  
  Exception: Concrete-encased electrodes of existing buildings or structures shall not be required to be part of the
  grounding electrode system where the steel reinforcing bars
  or rods are not accessible for use without disturbing the
  concrete.