That's the official upgrade disc. From memory, the official Firmware is ver 4.01, but I'm using a hacked 4.02 version from this guy
http://summittarcade.com/Sega.html
This isn't official though (looks like he's sold out anyway). You can get the official kits from Andy and giz10p.co.uk
I get the same issue with the pdf - it used to be in html about 6 months ago.
Edit: Managed to save as a text file, formatting is a bit screwy
FUJITA COMMUNICATIONS LTD
〒158-0093 東京都世田谷区上野毛4-34-8-101
#101 Kaminoge, 4-34-8, Setagaya-ku, Tokyo 158-0093
TEL:03-5706-4451 FAX:03-5706-4450
Email:Fujita11@jewel.ocn.ne. jp
To: Our customer
PCB LIST (Alphabetical Order)
BLAZBLUE (Rom for Type-x2)
BLOODY ROAR 2
BOMBERMAN
BOMBERMAN WORLD
BURIKI W/(64 mother bd)
CAPCOM FIGHTING JAM (CD&IC 246bd)
CAPCOM VS SNK PRO ( CD & IC Naomi)
CAPCOM VS SNK 2 (CD & IC Naomi)
CHINA DRAGON
CHODRAGON BALL Z (256 rom)
DONDEN LOVER
DONKEY KONG Jr
DUNGEONS & DRAGONS 1 (CP2 rom)
DYNAMIC GOLF (ROM)
ESPGALUDA II
FATAL FURRY (NEOGEO 64) (SUB)
FATAL FURRY (NEOGEO 64) W/mother bd
FATE (SOFT)
GALLOP RACER 1
GALLOP RACER II
GALLOP RACER III
GALS PANIC
GALSPANIC 3
GALS PANIC 4
GEM FIGHTER (Pocket fighter) CP2 rom
GUILTY GEAR XX ( CD & IC)
GUILTY GEAR XX # RELORD (Soft CD & IC)for Naomi
GUILTY GEAR XX SLASH (Soft CD & IC)for Naomi
GUNDAM DX
GUNDAM GUNDAM NEXT WITH 256 MOHER BD
GUNDAM VS ZION(ROM)
HAT TRICK HERO'93
JO JO
KING OF MAXIMUM IMPACT (TYPE-X 2soft)
KING OF98 ULTIMATE MATCH (Type-X rom)
KINNIKUMAN MASCLE GRANPRIX (rom 256)
KIRAMEKEKI STAR ROAD (F3 ROM)
KNIGHTOF VALOUR the SEVEN STAR SPIRITS (rom)
KOLLON (Soft for Gnet bd)
MACROSS
MAGICAL DATE
MELTY BLOOD ACT CADENZA ver A(CD&IC for Naomi)
28 Sept,.2012
Jp Yen
5,000 .-fighting
8,000 .-fighting
1,000 fighting
4,000 .-action
2,000 .-fighting
3,000 .-fighting
1,000 .-fighting
1,000 .-fighting
1,000 .-puzzle
3,000 .-fighintg
1,000 .-ocero
23,000 .-shooting
7,000 .-action
500 .-sports
35,000 .-action
1,000 .-fighting
2,000 .-fighting
13,000 .-fighting
1,000 .-horse race
1,000 .-horse race
1,000 .-horse race
1,000 .-position value
2,000 .-position value
3,000 .-position value
4,000 .-action
2,000 .-fighitng
2,000 .-fighting
2,000 .-fighitng
1,000 .-fighting
12,000 .-fighting
1,000 .-fighting
1,000 .-soccer
6,000 .-fighting
3,000 .-fighting
3,000 .-fighting
4,000 .-fighting
1,000 .-puzzle
2,000 .-action
1,000 .-puzzle
7,000 .-shooting
2,000 .-puzzle
2,000 .-action
MIGHTY PANG (cp2 system bd) (cp2 system bd) 2,000 .-puzzle
MOBILE SUITE GUNDAM 2,000 .-fighting
Mobile S Gundam Fedration vs Zion(Naomi rom) 1,000 .-fighting
Mobile S Gundam Federation vs Zion (CD&IC for Naomi) 1,000 .-fighting
Mobile S Z Gundam (CD &Dongle)for 246 bd) 1,000 .-fighting
Mobile S Z Gundam DX (CD&Dongle for 246 bd) 1,000 .-fighting
Mobile S Z Gundam Seed vs ZAFT (CD&Dongle) for 246 bd) 1,000 .-fighting
Mobile S Z Gundam Seed Destiny vs ZAFT II (soft) 1,000 .-fighting
MR. DRILLER 2 1,000 .puzzle
MUCHI MUCHI PORK 44,000 .-shooting
MUSHIHIMESAMA 35,000 .-shooting
MUSHIHIMESAMA FUTARI ver 1.5 45,000 .shooting
NAMCOCLASSIC Vol 1 18,000 .OTENAMI
HAIKEN (G-net soft) 1,000 .puzzle
OTENAMI HAIKEN Part -2 (G-net Soft) 100 .puzzle
POCKET GAL 1,000 .biliard
POP N POP (rom for F3 board 2,000 .-puzzle
POWERSTONE (Naomi rom) 6,000 .-fighting
PREMIER SOCCER 1,000 .soccer
PUZZLE BOBBEL 2x (F3 rom) 1,500 .-puzzle
PUZZLE BOBBLE 3 (F3 rom) 1,500 .-puzzle
PUZZLE BOBBLE 4 (F3 rom) 1,500 .-puzzle
KISEKINONIJIIRONOMACHI (CP2rom) 2,000 .-quiz
RAIDEN II 8,000 .shooting
RAIDEN FIGHTERS 10,000 .-shooting
RADILGY (NAOMI soft CD&IC) 14,000 .-shooting
RIVAL SCHOOL 1 8,000 .fighting
SAMURAI SPIRITS SEN (TYPEX rom) 10,000 .actionSD
GUNDAM  SLAMANDER 2,000 .action
SEABAS FISHING (STV rom) 100 .fishing
SEIBU SOCCER 1,000 .soccer
SENGOKU BASARA X(SOFT) 11,000 .-fighting
SHANGHAI 4 (Shanghai mateki buyuu) 1,000 .-puzzle
SHANGHAI GREATE WALL (STV rom) 1,000 .-puzzle
SHANGHAI SHORYUSAIRIN (G-net Soft) 1,000 .-puzzle
SHISENSHO 1,000 .shooting
SHISENSHO 2 1,000 .puzzle
SLASH OUT (NAOMI soft) 5,000 .action
SNK VS CAPCOM CHAOS (PCB type) 1,000 .fighting
SOCCER SUPER STARS 3,000 .soccer
SOUL CALIBUR 7,000 .fighting
SOUL CALIBUR 3 (soft) 29,000 fighting
SOUL EDGE 3,000 .fighting
SOTENRYU G-net soft 500 .puzzle
SPIKERS BATTLE (CD & IC Naomi bd) 2,000 .- action
SPORTS JAM (Naomi soft CD&IC) 800 .sports
S/F EX 4,000 .fighting
S/F EX PLUS 6,000 .fighting
S/F EX 2 5,000 .fighting
S/F ZERO 2 ALPHA (CP2 rom) 2,000 .-fighting
S/F ZERO 3 (CP2 rom) 4,000 .-fighting
STRIKER 1945 II 5,000 .shooting
SUPER MAJOR LEAGUE2001 (CD & IC Naomi bd) 500 .baseball
SUPER PUZZLE BOBBLE (Gnet rom) 2,000 .-puzzle
SUPER SLAMS 1,000 .basket
SUPER VOLLEY 500 .volleyball
SUPER WORLD STADIUM 2001 1,000 .baseball
TECMO WORLD CUP '98(STV rom) 1,000 .soccer
TEKKEN 2-B 4,000 .fighting
TEKKEN 3 6,000 .fighting
TEKKEN 4 (rom) 1,000 .-fighting
THE BATTLE OF Yu Yu HAKUSHO (CD &IC 256 bd) 3,000 .action
TOSHINDEN 2 3,000 .action
TWELVE STAG (GNET rom) 9,000 .ULTIMATE
TENNIS 1,000 .tennis
ULTRAMAN 1,000 .action
ULTRATOKON LEGEND 2,000 .action
USAGI NO TOHAI (GNET ROM) 800 .majong
VAMPIRE (CP2 ROM) 2,000 .-fighting
VAMPIRE SAVIOR 2 (CP2 rom) 3,000 .-fighting
V-BALL 1,000 .beach
volley
VERSUS NET SOCCER 1,000 .soccer
VIRTUA ATHLETE (CD&IC Naomi) 1,000 .sports
VIRTUA FIGHTER 4 (CD & IC Naomi 2) 1,500 .-fighting
VIRTUA FIGHTER 4 evolution (CD & IC Naomi 2) 1,500 .-fighting
VIRUTA FIGHTER 4 FINAL TUNED (CD & ICNaomi 2) 1,500 .fighting
VIRTUA NBA (NAOMI rom) 2,000 .basket
ball
VIRTUA STRIKER 2000 (NAOMI rom) 2,000 .soccer
VIRTUA STRIKER 3(NAOMI 2 soft CD&IC) 2,000 .soccer
VIRTUA STRIKER 2002 (ROM for Tryfoce ) 2,000 .soccer
VIRTUA STRIKER 4 (Japanese ver)CD&IC Triforce 2,000 .soccer
VIRTUA STRIKER 4 2006 (CD &IC Triforce) 2,000 .soccer
VIRTUA TENNIS (NAOMI rom) 2,000 .tennis
VIRTUA TENNIS 2 (CD &IC Naomi) 2,000 .tennis
V SHOOT SOCCER 1,000 .soccer
WORLD RALLY 8,000 .rally
X-MEN (cp2rom) 3,000 .-fighting
XMEN VS S/F (CP2 rom) 3,000 .-fighting
SNK 1 SLOT MV-1 2,000 .SNK
1 SLOT (SS) MV-1A 5,000 .SNK
1 SLOT (SS) MV-1B 5,000 .SNK
2 SLOT 2,500 .SNK
4 SLOT 4,000 .CP2
MOTHER BOARD 1,500 .EX
MOTHER BOARD 28,000 .F3
MOTHER BOARD 1,500 .KANEKO
MOTHER BOARD 1,500 .NAOMI
2 MOTHER BOARD 8,000 .PGM
MOTHER BOARD 4,000 .STV
MOTHER BOARD 5,500 .TYPEX
1 MOTHER BOARD 25,000 .TRYFORCE
MOTHER BOARD (Previous type) 8,000 .TRYFORCE
MOTHER BOARD (New type) 11,000 .CAPCOM
CONVERTER/without cables 2,500 .SEGA
CONVERTER/without cables 4,000 .GD
SYSTEM KIT 8,000 .***
CARTRIDGE
AERO FIGHTER 2 3000 .shooting
AERO FIGHTER 3 5000 .shooting
AGGRESSOR OF DARK KOMBAT(Gan Gan March) 2500 .shooting
ART OF FIGHTING 1,000 .-fighting
ART OF FIGHTING 2 1,000 .-fighting
ART OF FIGHITNG 3 3,000 .-fighting
BREAKERS 3,000 .fighting
FATAL FURY SP 1,000 .-fighting
FOOTBALL FRENGY 1,500 .football
KABUKI KLASH 2,000 .-fighting
KING OF MONSTERS 3,000 .action
K OF '96 1,000 .fighting
K OF '97 1,000 .fighting
K OF '99 800 .fighting
K OF 2000 1,000 .fighting
K OF 2001 1,000 .fighting
K OF 2002 2,000 .fighting
K OF 2003 (PCB type) 1,000 .-fighting
LAST BLADE I 1,000 .-fighting
LEAGUE BOWLING 1,500 .-bowling
MAGICAL DROP TABLE 2 1,800 .puzzle
MAGICAL DROP TABLE 3 3,800 .puzzle
METAL SLUG 6,500 .action
METAL SLUG 2 2,000 .action
METAL SLUG X 3,000 .action
METAL SLUG 3 4,000 .action
METAL SLUG 4 4,500 .action
METAL SLUG 5 (PCB ) 4,000 .action
NAM 1975 7,000 .action
NEO GEO CUP'98 1,000 .soccer
PANIC BOMBER 2,500 .puzzle
POWER SPIKERS II 1,500 .volley
ball
REALBOUT FATAL FURY 800 .fighting
REALBOUT FATAL FURY SP 800 .fighting
REALBOUT FATAL FURY 2 1,000 .-fighting
SAMURAI SHODOWN 800 .fighting
SAMURAI SHODOWN 2 1,000 .-fighting
SAMUTAI SHODOWN ZERO(5) 800 .fighting
SHOCK TROOPERS 2ND 5,000 .action
STAKES WINNER 1 1,000 .-derby
STAKES WINNER 2 1,000 .-derby
ST HOOP 1,000 .basket
ball
SUPER SIDE KICK 2 2,000 .soccer
WORLD HEROES 1,000 .fighting
WORLD HEROES 2 1,000 .fighting
WORLD HEROES PERFECT 1,500 .-fighting
POSTER
ARKANA HEART 2,000
DEATH SMILES 8,000
ESPGALUDA II 8,000
GUN SPIKE 2,000
HOT GIMIC MIX 2,000
IBARA 5,000
K OF 2003 3,000
METAL SLUG 3 2,000
SPECTRAL VS GENERATION 2,000
TEKKEN 6 4,000
KICK HARNESS FOR CAPCOM BD 350 .JAMMA
HARNESS FOR SEGA MODEL II 3,000 .JAMMA
HARNESS FOR SEGA MODEL III 3,000 .