Alright, I decided to reinstall freshly and give this another shot, I followed the step-by-step directions from miracle flame on this board:
http://forums.qhimm.com/index.php?topic=6238.0 , but I'm still having a few weird problems.
I installed everything in that order, and installed:
the k-lit codec/true motion codec and disabled in ffvideo decoder config
Saint's resolution 1.0 that had the chocobo patch integrated
YAMP with minigamespatch and transparentdiagbox
higher quality cloud
.6 NPC reconstruction patch
and advent avatars
I also reenabled windows98/me compat mode with 256 colors.
The problems I'm now having is the intro credits are completely warped and that IMMEDIATELY after the train fmv stops, the screen goes black and i hear very limited sound, see nothing except the text box. When I move forward, the battle screen commences and everything(except the music which I don't hear) is fine, then after that the game is fine. However, when I get to the next FMV after opening the door and look up to the tower, cloud like floats into the air.
edit: Maybe my cd isnt fully functional? It has some minor scratches. Also, in the game menu i cant adjust sound/volume settings, is this because I didnt install the yamaha synth and is this why theres no music perhaps?