"...but found JTAG ID code 0xFFFFFFFF"

Don't know if it helps but I have seen an error occurring in the programmer when you try to use the factory serial loader (installed in quartus programmer) to download the FPGA image in to the EPCS through the JTAG interface. I found that when I used the "Enhanced" version it sometimes failed. You can use the 'Default' one by going into the options in the quartus programmer and unchecking the 'use enhanced serial flash loader' tick box