Help setting up RFID reader with hard to understand schematic with arduino UNO

And what about a while loop with some sort of delay? say every 5 seconds The loop tests to see if that card is still "available" and records a time stamp of sorts.

No the code will be sent only once when the card is first presented, if the card is held against the reader the card's number is not repeated.

Again this was a "special" request I also implemented for a customer, but it is not the way RFID readers normally behave.

The chip that implement most Mifair RFID protocols has "card present" signal inside them and that could be used, but I don't think you have that sort of reader and you certainly can't reprogram the reader's software.