If you don't buy the RS package, you will always wish you had. The headlights and rims are well worth the money. I had the dual mode perf exhaust and I don't think I would have liked the car as much without it. The quad pipes are worth the money, and the sound is an added bonus. Manual transmission for sure, it is a muscle car after all.
Sounds like you're on the right track, just remember how hard black paint is to maintain. You may want to consider the ashen grey metallic (dark grey) to save yourself some pain
2013 2LT/RS V6 Manual 6-Speed w/ Cold Air Inductions Cold Air Intake, VMAX CNC Spiral Ported Throttle Body, 1LE Strut Tower Brace, Drake Bowtie Delete, SJM Autoprod Dash ABL kit, Side Marker Tint, Reverse Light Tint, Window Tint