The Fabric run script is part of the build script and should be added to each target and should be the last item in the build phases list.
e.g. Add the run script to the "Today Extension" target.
(note: it is not needed to add the Fabric details to the plist file for the "Today Extension" target).
The header file that is not found is related to the "Search Paths", 
and if the Fabric is installed via CocoaPods.
Make sure the Podfile installs it for both targets.
Run a "pod install" command after editing the Podfile.
Note: the two targets both include Fabric.
e.g.
   platform :ios, '9.0'
  # Uncomment this line if you're using Swift
  # use_frameworks!
  use_frameworks!
  target 'MyApp' do
  pod 'Fabric'
  pod 'Crashlytics', '~>  3.9'
  end
  target 'MoTodayExtenstion' do
  pod 'Fabric'
  pod 'Crashlytics', '~>  3.9'
  end
  post_install do |installer|
  puts("Update debug pod settings to speed up build time")
  Dir.glob(File.join("Pods", "**", "Pods*{debug,Private}.xcconfig")).each do |file|
  File.open(file, 'a') { |f| f.puts "\nDEBUG_INFORMATION_FORMAT = dwarf" }
  end
Note the post_install part in the Podfile, this step
updates/creates the xcconfig file that resides in the Xcode.
Look in the "Pods" folder within the Xcode application Project;
Inside these files are a couple of variables 
FRAMEWORK_SEARCH_PATHS 
GCC_PREPROCESSOR_DEFINITIONS 
HEADER_SEARCH_PATHS   
LD_RUNPATH_SEARCH_PATHS 
OTHER_CFLAGS 
OTHER_LDFLAGS 
PODS_BUILD_DIR
etc....
Specifically the "HEADER_SEARCH_PATHS" should include the path the
header file that could not be found.