It's worth whatever someone is willing to pay you for it. Typically anywhere between $300 and $1000. Depends on it's condition. If it was behind a 289 and it was a true 390 Toploader, then there's going to be wear and/or broken parts in the input end of it, if it was run any length of time.
I never trust the case ID. The cases are some what universal and someone could have swapped the longer small block input shaft into it. It would then work fine behind a 289 (especially if it still has the wide ratio gear set.) Also note that different length output shafts and tailshaft housings also swap easily too.
I just sold one that was from a 289 full size. I swaped the main shaft and tail housing to make a "short Mustang" tranny out of it. I had a new Hurst comp-plus on it. I sold it on Craigs list locally for $600 and the people almost ran over each other to get it. I saw my old tranny on ebay a week later and it sold for $850. take off $200 for the shifter and i would say theres your price. If it was from a Mustang an the numbers all match what some one is looking for, I'm sure it would fetch a cool grand
Matching number concours people will spend what it takes. It's hard to find toploaders that came from the factory in the mustangs. Most were 3 speeds. Most 4 speed Mustangs were done in someones garage