It is hard to follow without linking to the trouble "Dave" ran into.
I've never had trouble recovering corrupt SPI flash BIOS, but I do the programming out of site.
My programmer is a Xeltek SP500P the recommendations for use are to add 30pF capacitors between SO and /CS to ground, I have found this to often be needed.
For ISP they also recommend adding a bypass capacitor of 20 to 100nF (Vcc-GND across I.C. or SPI header) .
Once you have been able to flash, think of replacing battery and CLRCMOS jumper in the right position.
Hope that helps.