Thank you for sharing all of this detail. Unfortunately, I am pretty buried at the moment so I don't have time to go through the code that you were kind enough to offer. Based on the pictures, I would consider grounding your signals closer to their connection points and when I have to use this type of wiring, I try to twist a ground with each signal to help reduce ESL, which reduces ringing and opportunity for other signal integrity issues.
The next thing that I would do is loop my code on the PROD_ID read, while using a scope to validate the SPI basics. This is discussed in the ADIS16480 Datasheet (rev C), in the READING SENSOR DATA section. Figure 16, on page 12:
http://www.analog.com/static/imported-files/data_sheets/ADIS16480.pdf
Here are some additional things that might help.....
ADIS16488 communication with Arduino:
https://ez.analog.com/message/71797#71797
SPI Basics (for a different product, with similar SPI operation):
https://ez.analog.com/message/44238#44238
I hope this helps and look forward to your feedback/response on this forum. Good luck!