Then this is your only option: in 1964 load the game, load the save state, in-game enter the subscreen and hit save. [for zelda only]
Go into your 1964 folder and then to the save folder
Take a file named something like this: THE LEGEND OF ZELDA-EC7011B77616D72B.sra
Copy it over to Project64's save folder, rename it to THE LEGEND OF ZELDA.sra there.
Load the game in Project64.
Similarily you have to take the eep files for other games, make sure to get rid of the -LLLA89354654 looking things on sra and eep after you place them into project64's save folder. Same for fla files.
If this doesn't work then you will have no choice but to play through the game again, I don't see any reason why it wouldn't... but keep in mind 1964 0.9.9 is not Project64 1.6, they don't think alike all the time, which is why a savestate might fail.