Please refer to this thread Is there any examples of updating Xilinx FPGA bit file through FX3? where the customer was able to program the Cyclone 4 FPGA with AN84868 application note.
Please refer to the FPGA documents to check the pull up resistor values.
The FPGA configuration Utility has an option for all files (*) , so you can try sending the .sof file using the utility
utility.png 14.1 K