not sure what your argument there is...i just read the manual you posted and it says absolutely nothing about it being the same link. it says that vaati returned and kidnapped princess zelda who was saved by a childhood friend who defeated vaati or so everyone thought. there was obviously plenty...
what would make you think they go close together? thats just as good of a question as the one you asked.
FSA pretty much HAS to come before ALTTP. in ALTTP you can go to the four sword shrine and see the broken four sword and the opened chest. this shows that ganon escaped. ganon was sealed...