fpga4fun.com

You can't, that's an input to Dragon, the PC drives the clock.

1. use a GPIO close by to solder a wire as short as possible
2. get the GPIO assignment right so no need for a resistor

There is no short protection.
You could potentially fry the FPGA... but in practice the FPGA usually survives this kind of abuse.

You could put a 100ohms resistor first and remove it later once you know your assignment is good.

Yes, the resistor will affect the signal significantly.