Thanks for everyone's suggestions.

BRAKE PEDAL CLICKING/PULSING
The original clicking/pulsing was coming from the brake pedal. I checked the brake fluid level and it was low, adding additional fluid resolved the problem. It must have been some combination of low brake fluid and humidity.

SHIFTER CLICING
As for clicking under the shifter, I noticed that this only occurs when the car is in Park and when I release the brake. Is there any way to fix this? By the way, What's a "dee-dee-dee" VX?