I’ve gotten it from a few places… some I’ve taken from Netflix (Nihongonobaka has converted a bunch of Netflix subs in japanese into .srt files and put them here).
Some I’ve transcribed myself from this guy’s let’s play channel (he has the habit of writing a lot of what he says on screen)
I’ve also made some from persona 4 using this script browser and cropping out mp3 files from let’s play videos…
I’ve used some amateur-created ones as well, but those may well have the same problems your have.
EDIT: Oh yeah, I found some here as well, and also found some subbed Japanese TED talks. (Though I don’t know how legit either of those sources are)