He just left and because my basement is finished and he has a busy day and he was running late; he wouldn't be able to do it for me today. As a compromise we used the fan control wire (I don't use this feature, I use ceiling fans if it is stuffy) as a common.
I am not reliant on the batteries, and I have heat and air. He moved the white wire from C to W1 and blammo - furnace works. He said that he was training a new guy and he assumed that he hooked the wires up right.
I could call Sears and tell them that I want a wire with 8 wires ran so I can get my fan control back; but I think I would rather shoot myself in the foot.
He did teach me a trick for getting the new wire from the wall by my stat to the furnace. He said block off all the other returns, tie a grocery sack to some fishing line and turn the Air on and let the return suck the bag down to the furnace. He emphasized that you should leave the filter in to catch the bag - then you have a handy dandy pull string to attach to your wire. I will do that some weekend in the future.
Thanks everyone for your help on this issue.
He did mention that Sears had called him and told him to "hold off" on coming out - I don't know what all that is about.