All went well until I tried to add a timestamp
You forgot to describe the problem.
additionally the SD Card CS, SCK, and MOSI lines are buffered with a CD4050 chip
Why the buffer chip? A bidirectional level converter would make more sense, as would using a 3.3V Arduino. Please post a hand-drawn wiring diagram.
We recommend to get all the parts working individually before putting them together. Have you separately been able to read and write to the RTC without problems?