Does "step" here mean "stage", or "phase"?

What's she mean by "not too shabby for Rachel?"

"Not too shabby" means fairly good or quite good. Her name is Rachel. So, when she said, "It's not too shabby for Rachel," she means that "It's quite good for me." Ex. We stayed at a cheap hotel but it's not too shabby. Ex. I got lost on my trip! However, I saw this handsome guy who gave me a tour of the city. My experience was not too shabby.

What's "trigger" mean?

"Trigger" is both a noun and verb. In this case, to "trigger" means to cause something (like a process, event, or situation) to happen, start, or exist. The speaker says "triggering the process of ... plaque buildup" to mean "prompting/setting off the process of plaque buildup Ex: The school shooting was the trigger for mass protests in cities around the country. Ex: If you add these two chemicals together, you will trigger a reaction.

What's "by the time" mean and when's it used?

"By the time" is a phrase used to say that something has or will happen at the time something else happens. Ex: By the time I was 23, I had received my undergraduate degree. = At the time of turning or being 23, I had received my undergraduate degree. Ex: We'll be home by the time the food arrives.

What is 'waterlog'?

"Waterlogged" describes something that has become soaked or filled with water. Ex: The homes were waterlogged after severe flooding. In this case, however, the memory circuits of the brain are described as being "waterlogged" in a metaphorical sense, since he compares the brain to a sponge here. When a sponge is too soaked with water, it cannot soak up any more water just like a brain cannot hold any more information when it is too full already.

I've heard there's a "wacky hair day" in western culture. Then does it somewhat related to the "bad hair day?"

Primarily in the USA, schools and public institutions would occasionally have a "wacky hair day", which is a day where people were expected to style their hair in "wacky" ways and would not be judged negatively for it. There is a slight relation to "bad hair day" as an expression, specifically the name of the event being inspired by the expression, but "wacky hair day" itself is not used as an expression. It is uncommon for institutions or schools to have "wacky hair days" anymore because many people, especially younger people, chose to style their hair in unconventional ways to begin with. Ex: Did you see how she came to wacky hair day? She looked so wacky! Ex: I'm having such a bad hair day, good thing it's wacky hair day at school so no one will notice!