Match the name on your application to that on your passport, not ECA. If you have different names on different documents like ECA and reference letter etc then attach a 'one and the same person' affidavit.
But your given names do include your middle name, so you should have added it from the start. This question is asking what is on your birth certificate/legal name.
Either way, add a note in your LOE and hope it's fine.
You can get the affidavit from a notary nearby. Depending on which country you're in the process to get an affidavit will be different. So ask around and figure it out.
Yeah just write an loe if you're changing any information post ITA. It will be fine.