Dark Blue is the field (to regulator) Black/Wht is the sense wire (to regulator) The heavy terminal connects to the battery positive.
Chad, you said "now my battery doesn't charge". Does this mean that it charged okay before you set out to correct some wiring problems? If so, check all of the connectors. The contacts can slide back into the housing and end up not making connection. Also, the contacts are crimped on and the crimp can go bad from disturbing old wiring. You will find connectors like this at the regulator, alternator and the main firewall plug. When you mate electrical connectors, you should put some dielectric grease on them. This will prevent corrosion from deteriorating the connection.
You can repair the original alternator if there is a problem with it. The brushes are available for around $5. The brushes should be replaced on any car with over 75,000 miles on it just to avoid the walk home one day. The diode trio is also readily available. Lastly, they sell new bearings for the original alternator. You can restore the original alternator to new reliability with inexpensive parts and a bit of work.
The electro-mechanical voltage regulator can be replaced with a solid state equivalent. Standard Motor Prouducts lists their VR-103X as a form/fit/function replacement. The reliability of a solid state unit will be superior.
Unless you need more power for audio gear, I would recommend that you fix what is there rather than swap in different parts that alter the wiring configuration.
You can make the headlights brighter by installing the Halogen replacements. A larger alternator will not make the lights brighter at cruising speed. A larger alternator will prevent headlight dimming at idle.
