Hey dood, I did a little more checking for ya and it seems to me that with only 3 inches missing from the harness, I would go ahead and crimp new ends to it and run it. The longer the harness, the more resistance and voltage drop the thermocouple signal is going to encounter. According page 3 of this...
www.turbodieselregister.com/EGT_EVAL.pdf
your gauge will be calibrated to take into account a given amount of resistance based on the harness length. With 3 inches missing, I would spectulate that the gauge would read only slightly hotter than actual EGT and if anything, you'll be monitoring on the safe side. My $.02 and worth about the same.
Again, just my opinion but I don't look at my pyro as gospel. For me it's just a reference point...I know what temperatures to expect on the flats and on the climbs. I know where it makes power (unmodified 3BII) and where it bogs. I use the EGT gauge to watch for out of the norm spikes on long climbs, headwinds, etc or if I ever get around to turbo-ing and turning up the fuel. Once I finish the install on my wife's 1hz, I'm not going to expect the numbers to be exactly the same.
HTHs