I know for a fact that 90% of FFT's songs aren't yet looped properly (rather, I don't believe he's posted the looped versions yet), so I had to cut the silence out of all the tracks I got from him. They all loop seamlessly in winamp now.
As for the missing files, here's a guide I wrote up some time ago that should help you determine what you're missing:
aseri = "Hurry!"
aseri2 = "Hurry Faster! (Hurry up!)"
ayasi = "Lurking in the Darkness"
barret = "Barret's Theme"
bat = "Fighting (Let the Battles Begin)"
bee = "Honeybee Manor"
bokujo = "Farm Boy"
boo = "Lifestream"
cannon = "The Makou Cannon is Fired~Shinra Explodes" (medley)
canyon = "Cosmo Canyon"
cephiros = "Those Chosen by the Planet"
chase = "Crazy Motorcycle"
chu = "Those Who Fight Further"
chu2 = "J-E-N-O-V-A"
cinco = "Cinco de Chocobo"
cintro = "Those Chosen by the Planet" (heartbeat intro only)
comical = [Unused in game]
condor = "Fortress of the Condor"
corel = "Mining Town"
corneo = "Don of the Slums"
costa = "Costa del Sol"
crlost = "Tango of Tears"
crwin = "A Great Success"
date = "Interrupted by Fireworks"
dokubo = "Underneath the Rotting Pizza"
dun2 = "Chasing the Black Caped Man"
earis = "Aerith's Theme"
earislo = "Flowers Blooming in the Church"
elec = "Electric de Chocobo"
fan2 = "Fanfare" (full)
fanfare = "Fanfare" (opening)
fiddle = "Fiddle de Chocobo"
fin = "World Crisis"
geki = "Debut"
gold1 = "Gold Saucer"
guitar2 = "On the Other Side of the Mountain"
gun = "Shinra Army Wages a Full Scale Attack"
hen = "Who Am I?"
hiku = "The Highwind Takes to the Skies"
horror = "Trail of Blood"
iseki = "You Can Hear the Cry of the Planet"
jukai = "Forested Temple"
junon = "Off the Edge of Despair"
jyro = "Steal the Tiny Bronco"
ketc = "Cait Sith's Theme"
kita = "The Great Northern Cave"
kurai = "Anxious Heart"
lb1 = "Birth of a God"
lb2 = "One Winged Angel"
lb2_awe = "One Winged Angel" (AWE)
ld = "Judgement Day"
makoro = "Makou Reactor"
mati = "Ahead On Our Way"
mekyu = "Reunion"
mogu = "The Moogle Takes to the Skies" (first 15s of "The Highwind Takes to the Skies")
mura1 = "Parochial Town"
nointro = "Those Chosen by the Planet" (no heartbeat intro)
oa = "Opening~Bombing Mission" (medley)
ob = "Bombing Mission"
odds = "Place Your Bets! (Racing Chocobos)"
over2 = "Continue"
parade = "Rufus' Welcoming Ceremony"
pj = "Jenova Absolute"
pre = "Final Fantasy VII Prelude Theme"
red = "Red XIII's Theme"
rhythm = "Turks' Theme"
riku = "Shinra Explodes" (part 1)
ro = "The Countdown Begins"
rocket = "Oppressed People"
roll = "Staff Roll"
rukei = "Sandy Badlands"
sadbar = "Mark of the Traitor"
sadsid = "Sending a Dream into the Universe"
sea = "Secret of the Deep Sea"
seto = "Great Warrior"
si = "Shinra Explodes" (part 2)
sid2 = "Cid's Theme"
sido = "It's Difficult Standing on Both Feet, isn't it?"
siera = "If You Open Your Heart"
sinra = "Shinra Company"
sinraslo = "Infiltrating Shinra Tower"
snow = "Buried in the Snow"
ta = "Final Fantasy VII Main Theme"
tb = "Final Fantasy VII Main Theme" (from middle)
tender = "Holding my Thoughts in my Heart"
tifa = "Tifa's Theme"
tm = "On That Day, Five Years Ago"
utai = "Wutai"
vincent = "The Nightmare's Beginning (Vincent's Theme)"
walz = "Waltz de Chocobo"
weapon = "Weapon Raid"
yado = "Goodnight Until Tomorrow"
yufi = "Descendant of Shinobi"
yufi2 = "Stolen Materia"
yume = "Who Are You?"
Pay heed to this list and look for files that you don't have. Some are doubles, some are edited copies. You're gonna have to cut some of the mp3's to get the full list. If you're not sure where to cut, look for the original MIDI's online (they're easy to find) and play em.