The FPGA JTAG seems to be forming a chain with the ASICs and CPU JTAG (excluding XCF04S). This chain could be accessed from the Mictor connector, but this circuit (the chain) is not fully implemented. Looks like Agilent only fully assembled this circuit, if necessary, adding and/or removing some components (probably some resistors). I think that the Mictor connector is mounted, because add it manually later must be hard.
The JTAG connector J2600 is exclusively for the XCF04S, but CPU also accesses this port.
The connector J2400, also seems to be connected to the CPU JTAG.
TMS and TDI (FPGA) are connected to the ASICs U29000, TDO ends on a open jumper between the FPGA and the Mictor, and I have been unable to find where TCK goes.
However I don't think that it matters...
Also seems that the front end is controlled only by the CPU (at least a part).