Error: CONF_DONE failed to go high in device 1.

Ok, I went back to the first page and reviewed all posts and things done so far - did also "googled" around and hooked my scope to the pins you plotted... One thing is the TDI Pin - this should not really be just spikes as shown as this pin is used to push the information to the FPGA. It also seems that the "Auto detect" function does not use the TDI at all, as the ID Code is read by combination of TCK, TMS and TDO only, thus any problem on the TDI line would not be recognized at this stage. Maybe it is worth to have another look at the physical connections of TDI.. Should be pin9 of JTAG Header to Pin H4 with only a pull up connected...