I'm pretty busy so I can only do a cursory search. I cannot find the source I originally read this on, however I will try to find it when I am at home.
Here's what I could find via a preliminary Google search on my phone:
From drugabuse.gov [0]:
> In the aforementioned study, abstinence from methamphetamine resulted in less excess microglial activation over time, and abusers who had remained methamphetamine-free for 2 years exhibited microglial activation levels similar to the study’s control subjects. Another neuroimaging study showed neuronal recovery in some brain regions following prolonged abstinence (14 but not 6 months). This recovery was associated with improved performance on motor and verbal memory tests. But function in other brain regions did not recover even after 14 months of abstinence, indicating that some methamphetamine induced changes are very long lasting.
Here's a graphic they included [1].
This is another source [2]:
> Stopping drug use doesn’t immediately return the brain to normal. Some drugs have toxic effects that can kill neurons—and most of these cells will not be replaced. And while changes to connections between neurons in the brain may not be permanent, some last for months. Some research suggests the changes may even last for years.
I cannot find the studies these articles cite, but I'll try to find them later.
This is related, but is not specific to stimulant or methamphetamine use:
Delta-FosB, an enzyme that is critical to achieve an addiction state in the brain, has a half-life of ~208hr [3]. Multiply that by the standard 7 half-lives to estimate significant elimination, and that alone yields a maximum of 60 days until it is cleared. This enzyme is key in drug and behavioural addictions.
This paper [4] speculates about changes in the brain that last longer than the time it takes to eliminate elevated Delta-FosB levels in the brain.