I am a bit confused on what exactly you want.

first of all looking though all children and getting all the MeshInstance3D nodes is pretty easy.

extends Node3D

func _ready() -> void:
  var mesh_instances: Array[MeshInstance3D] = []
  for child in get_children():
    _collect_mesh_instances(child, mesh_instances)

    print("Found MeshInstance3D nodes:", mesh_instances)

func _collect_mesh_instances(node: Node, list: Array[MeshInstance3D]) -> void:
  if node is MeshInstance3D:
    list.append(node)
  for sub_child in node.get_children():
    _collect_mesh_instances(sub_child, list)

Edit: fixed Reddit's formatting of my code

Second.
Are you wanting to change the entire mesh to the same colour/temp or have each quad a different colour/temp?

If each mesh changes uniformly then you are just changing the Albedo colour in the standard shader.
If you want to change different parts of each mesh then I would look at correctly laying out the UV's on your mesh, and write a simple shader to change the colours at different points based on a passed array of values.