The only functional pin on the data CPLD I can't find connected is pin 4
That's part of the serial link between the two CPLDs, used for implementing autoconfig: The 144-macrocell CPLD does not have any data lines, but all the required address lines. So in order for logic to answer with data to an access is to shift the data into the data CPLD and then terminate the access. So the data CPLD does not only pass/latch data to/from the Amiga, but also implements a shift register, which must be able to drive both the CPU-side and the Amiga side (note that Autoconfig also works when the card is in "memory only" mode).
Pin#4 is connected through R13 to Pin#95 of the '144.
and wait for it...
CLK.. (Seriously... I *really* should have spotted this one sooner!! )
Your bodge wire connects CPU clock to FPU clock. That's not a standard connection; the FPU clock is only equal to CPU clock if you close the FPU clock solder-jumper on the top side of the board (just above the oscillator space). If the oscillator is assembled, then you're shorting the oscillator-out with the clock-output of the main CPLD, possibly damaging the '144.
Local D31 flappin' in the breeze at least indicates "not shorted anywhere". Or is that yellow noise line not D31, but the flat green one?
The local D31 should be connected to:
Pin #94 of the data CPLD
Pin #23 of U4 (SD-Ram Data bus driver)
Pin #N1 of the CPU
Pin #J5 of the FPU
Noise would really indicate that something in the CPLD itself is wrong. The pins are configured as "keeper", which is the Xilinx way of "faking" an input hysteresis, but it really helps getting the board stable with ageing power supplies (and sometimes even with Keelog/Electroware PSUs, which I highly recommend to send back due to false advertising claims).
All those open connections on your baord are weird. I don't see that the CPU has been removed (or at least it was very nicely soldered back). I have no idea how so many traces could fail - even if some aggressive cleaning fluid had been used, the solder stop should have protected the board.