回答“Focus Indicator does not show up AF will not lock with viewfinder”The AF system used when in live view is entirely different from the one used otherwise, that is why it is working even when there seems to be something wrong with your AF system. The live view system only uses the features of the sensor, no secondary components. The 'regular' AF uses the system as described by Flying Dutchman.
回答“The colors in my photos have been off by a couple shades?”Though I agree with the answer of the Flying Dutchman, remember that if you use auto you may get changing white balance (and thus apparently different colours) even in a number of shots taken only seconds apart. The camera then assesses the situation for each shot separately, and if the light changes between shots it will produce different results.