So the 25th anniversary Charvel was shortly after Fender bought out Charvel. They were able to finally use the Fender headstock again, and they were a custom shop limited run of 86. WAY overpriced, but Fender was trying to go for the "collectible" pricing kind of like how Gibson does with Historic Les Pauls.
They would do this again a few years later later with the Legacy model (even crazier starting pricing that quickly dropped).
The 08/09 USA pro mods are not custom shop guitars, even though some feel like similar quality (my best one was pretty on par with a CS). They were mass produced with a much lower starting price than a 25th anniversary or any CS.
As mentioned, this market has everything crazy high right now. $3500 is not completely out of line in this market, but once supply picks back up and people cool on their spending, a lot of people are going to be selling at a loss. This is not a buyer's market.
My rough guess is closer to $2500ish or slighty north of that in a normal market.