Look for the serial tag on the right side of the transmission, right in front of the right brake. It should be there or on the dash where you have already looked.

Korves Oliver ( <!-- w --><a class="postlink" href="http://www.korvesoliver.com">www.korvesoliver.com</a><!-- w --> ) has patch panels to fix the hoods on the Fleetline tractors. 

For the other hole, Oliver offered a retrofit kit to put a pre-cleaner above the hood. So no, it wasn't originally there, but it was most likely a factory supplied package. Whether you want to return it to factory is up to you, but it was an official Oliver update.