MacOS – Replaced Macbook Pro keyboard with US-layout, now cannot type ~/` on external keyboard

Regarding the extra key to the left of the z, you should get that with any "ISO" keyboard sold in Europe. In the US, keyboards are "ANSI" and are missing that key. Other countries may vary. See this note:

http://support.apple.com/kb/HT2841

KeyRemap4MacBook also supports device-specific settings:

<?xml version="1.0"?>
<root>
  <devicevendordef>
    <vendorname>KINESIS</vendorname>
    <vendorid>0x05f3</vendorid>
  </devicevendordef>
  <deviceproductdef>
    <productname>ADVANTAGE</productname>
    <productid>0x0007</productid>
  </deviceproductdef>
  <item>
    <name>modifierkeys</name>
    <identifier>modifierkeys</identifier>
    <device_only>DeviceVendor::KINESIS, DeviceProduct::ADVANTAGE</device_only>
    <autogen>__KeyToKey__ KeyCode::CONTROL_L, KeyCode::FN</autogen>
    <autogen>__KeyToKey__ KeyCode::FN, KeyCode::CONTROL_L</autogen>
    <autogen>__KeyToKey__ KeyCode::COMMAND_L, KeyCode::OPTION_L</autogen>
    <autogen>__KeyToKey__ KeyCode::OPTION_L, KeyCode::COMMAND_L</autogen>
  </item>
</root>

You can see the vendor and product IDs from EventViewer.app. If it can't remap any keys on the external keyboard, try uninstalling other keyboard or HID drivers.

See the source for the key code values and predefined settings.