Excellent !! Great way for us to start off the day with your positive note :)
Now with the working JTAG (XTAG) interface, you should have full control over the local SPI flash device for R/W access so you should be able to test with local blinky code, etc. Then as you are stating to test with both CPUs installed, you could create custom s/w to communicate between the 2 devices using srinie's AN01024 (see above for URL for this appnote). So it should now be possible to perform the communication with your PCB as-is since you allowed for local SPI flash devices. That is clever thinking and your safety net. Exciting stuff - good luck !!
PS: When and if you re-spin the PCB layout, do consider to use the XMOS recommended ports for multi-CPU designs which will then allow you to remove the 2nd SPI flash (as a cost reduction).
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