Transmission Noise problems of the 2003 Toyota Prius

After a series of problems with the Prius engine the local Toyota dealer informed me that I needed to have the car's transmission replaced. Naturally the vehicle is no longer covered by its warranty. Back ground: 2003 Prius, odometer reading 116,289. On 12/22/2008, I started the car and the check engine light appeared. I was towed to the dealership. The dealership informed me that the gasoline engine shut down and the battery ran out of power. The dealership could not reproduce the problem. On 12/27/2008, I started the car and the check engine light appeared again. I had the car towed to the Toyota dealer. The dealership discovered oil in the intake manifold as per a TSB. The dealership did not charge me for part of the repairs. On 01/04/2008, I was driving when an intermittent grinding noise began on both braking and acceleration. I found that the noise disappeared if I braked and accelerated extremely gently. I immediately drove to the dealership. When I went to the dealership, I was told that the problem could be as simple as a shim in the braking system that may have slipped out of position. I authorized an estimate of $52. 52. The following day, a service person of the dealership called and told me that the brakes were fine but that the problem could be resolved by changing the sparkplugs. I orally authorized an estimate of about $150. 00 (I don?t remember the exact amount. ). The service rep called me later that day (1/5) and explained that my problem wasn't?t really the sparkplugs but that the car's transmission needed to be replaced. The estimate for the parts and labor for this repair would be approximately $2,000. The service rep informed me on 1/6/2008 that a mistake was made and cost of the new transmission alone would be $5,000, with other parts, labor, and the cost of a rental car, the final estimate for repair was around $7,000.