I think we've exhausted the theories on who Red John is based on evidence, so here's my theory on how Jane catches Red John based on evidence...

Jane chases Mcallister into the Park. Dumps muffins all over him and he gets mauled by pigeons. Mcallister has panic attack from his fear of pigeons and faints. Patrick Jane ties him up and holds him down. Tom wakes up and Jane slices him up. End Scene.