As far as the harness, the price seems to be in the ball park of what others have paid, maybe they have paid just a bit less.... If I remember correctly from others posts about it. If you search for wiring harness, or engine harness, you should find a lot of people have discussed this and its costs. Perhaps you can get stats on how many good will repairs have been done on the harness for your car's year and model, to help you in your fight to get it done under warranty or for free.
Does your warranty state it covers electrical? If it does then why would they deny to do the wiring harness, and is the warranty going to cover your head gasket? If not, what the hell good is the warranty?
As for the Head Gasket, I think the average cost is anywhere from $1000 to $1500 depending on what else has to be done and of course where you go. But I have not had it done myself, so My prices may not be even close to what it really costs.
IF they are changing the head gasket are they going to be doing a valve job too or is it just to replace the gasket? If its just the gasket, you should find out about doing the valves at the same time, It can't hurt to do them then, once the head is off, you might as well get the valves done.
I'm not a tech, and I have no idea on the actual prices, but from what I have read on this site, and from what I can remember, that is if my memory serves me corectly, it is within the average price of what you got quoted.