Voltage Regulator Question

Great thank you I appreciate it. Should the new voltage regulator help with flickering/dim headlights and all that? Everything is pretty much stock on my car except my MSD ignition system.
Maybe not. The battery in the trunk presents a whole new set of possible issues. What size of + wire did you use to run to the battery in the trunk? And how did you run the battery - to the car? Bolted to the trunk floor? Is there an inline battery switch?

The battery serves a purpose beyond energy storage as what is called a 'ballast' for the alternator and the electrical system. This means that if for any reason the alternator tries to put put too much voltage for a moment, then battery clamps down that 'surge' and keeps the system voltage stabilized. If the bettery is remotely located, and the wire guage is too small and/or the + and - connections are not very good and very low resistance, then the ballast effect of the battery is limited or lost and there can be significant voltage fluctuations in the electrical system and possible short lives for the alternator. Flickering lights can be due to this.

Rear mounted batteries are great for weight transfer and better wieght balance in some racing apps, but for street cars, it is something that has to be done well or you create new problems.