2005 Silverado Transmission/Computer

Had my transmission replaced back in October when the truck quit going into Overdrive. Went out again last weekend and put it back in the transmission shop. Transmission shop replaced transmission with a brand new one including torque convertor. Shop now thinks the truck needs a new "computer" which is $500 at the dealership plus "programming" fees of around $100. Is there ANYWHERE else to get that computer or can the computer just be re-programmed? I don't see how a vehicle that is only 3 years old and only has 60,000 miles can have so many problems. My CD player doesn't work, A/C won't blow on the "5" setting and the lights/chimes/etc. are always weird about not working/working or going at random times. This sucks!