If the engine block numbers match the vehicle vin number, most likely somebody got a little frustrated with the Manual, and replaced it with an Automatic.
Although, you've got to be a little odd to want to replace a manual with an automatic, it happens.
I'd assume that if your engine does match your vin, then you do have the original engine, but someone just changed your vehicle over for their pleasure.
Looks like you'll be dropping out the transmission, and finding yourself a manual replacement if you want to go back to stock.
-Brad