Programming a custom board without flash memory

Could you do a simple design in VHDL or Verilog with just a counter that flashes a led? At least you would know that way if the clock is working.

I'm not sure that connecting the reset signal to vcc is a good idea. I think the SOPC system needs its reset signal to start correctly. If you don't have an external reset on your board, you can use an internal reset generator based on a counter, as suggested in another thread in this forum.

You don't need a second clock for the JTAG interface, it is provided by the USB Blaster.