Can Di2 only be tested as a complete setup?
Okay problem solved. Apparently the NOS cable set that I bought came with an SM-EW90-A with really old firmware. After installing E-Tube Project v3.4.5 and restarting my laptop, I was able to update the junction box using SM-BCR2. The RD works without the FD mounted and I was able to make initial adjustment while waiting for the FD.
Thank you for all your comments and hopefully we learn something new everyday!