I'm no Beach Boys expert, but here's what I know.
I've heard both the 1990 CD that contained only a mono version of the album and the more recent 1999 CD that contains both the original mono version and a more recent stereo version. Brian Wilson was, I believe, deaf in one ear so wasn't really able to judge stereo recordings and so mixed it mono. I believe both CDs contain a track or two not present on the orignal album, but I'm not positive.
I think the 1999 version sounds better, but a couple of times I've had CD players not want to read it (maybe because it is so long--just a shade under 80 minutes?). I also know there is a 4 CD box set covering the pet sounds album (the 1999 CD has the same mastering as the set I believe), but I"ve never heard it.
I hope this helps.