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Especially for the VCCINT regulators I'd tend to stay on the positive side of the tolerance, as there will be non-neglegible voltage drops across the traces and FPGA pads. Remember that VCCINT directly affects achievable hashrate. Up to 1.26V are allowed here (1.32V absolute maximum), so I'd probably go for 1.25V for this rail if the regulator feedback comes directly from the FPGA's pads.
To take advantage of this you'll need to define the guaranteed minimum voltage in the UCF file.
I think moving the resistors below the FPGAs is a given by now. But if we increase the core voltage to achieve higher clock rates, then I would ask how close we want to cut it: is there a risk of having any EMF mess with the trace from the resistors to the switcher, so that the switcher runs at a too high voltage? What about required or suggested resistor tolerance: is 1% sufficient?
And our of curiosity: what is the gain in terms of clock rate for a voltage increase of 0.05V? I am willing to take ISE estimates after whichever stage you feel is remotely reliable.
IIUC the resistors shouldn't be below the FPGA, but instead as close to the switcher as possible, but fed from a trace that's coming back from one of the FPGA VCCINT pins. Also remember that this will only compensate for the losses on the VCCINT path, not the GND return, so the effective voltage will still be a bit below the programmed value. Ask one of our more experienced electrical engineers regarding how close to cut it, I'm just a computer engineering student. I just wanted to suggest to stay on the positive side of tolerance, as the suggested values were on the negative side, which doesn't seem like a good idea.
I don't think ISE even takes these values into account before the PAR stage, so you'll probably have to do a full synthesis run without timing constraints enabled or even step constraints to check the maximum achievable clock for both voltages. I've done a quick search on the web and didn't find anything even remotely related, so we'll probably have to analyze this ourselves.
Are there any components on the back of the board as well? If yes, would you mind posting a picture of the back side of the board as well? I'm a bit worried by the small number of capacitors that I'm seeing on the front of the board...