List of Pokemon Masoleum Shadow Pokemon/Gift Pokemon/TM Alt.

List is complete to my knowledge, may update if anything new pops up.

Starters
Espeon: Now knows
Confusion/Shadow Sneak/Reflect/Hypnosis
Umbreon: Now knows
Thief/Low Sweep/Wish/Helping Hand <has Shield Dust as its ability>

Gift
Plusle: now knows
Thunderbolt/ThunderWave/Sketch/Sucker Punch <has Huge Power as its ability>

Shadow Pokemon (in order of appearance) and moves
*[Moves in Brackets are the purified moves that replace Shadow Rush]
*<abilities in symbols are new abilities>*

(Phenac City)
Shadow Murkrow Lv 30 [SuckerPunch]/Feint Attack/Confuse Ray/Brave Bird
Shadow "Combuskin" 30 <Speed Boost> [Brave Bird]/Blaze Kick/Mirror Move/Jump Kick
"Marshtomp" <Swift Swim> [Stone Edge]/Muddy Water/Mud Slap/Earth Power
"Grovyle" lv 30 <Lightningrod> [X-Scissor]/Leaf Blade/Leech Seed/Dragon Claw
"If any of the following Pokemon are KO'd, you can find them later either Post-Credits in the Mayor's House or at Realgam Tower (for the starters)

(Pyrite Town)
Shadow Shroomish lv 30 [Low Sweep]/Giga Grain/Leech Seed/Spore
Shadow Electrike lv. 30 [Crunch]/ThunderBolt/ThunderWave/Flamethrower <Intimidate as Manetric>
Shadow Swellow lv 31 [BraveBird]/Airslash/Assist/ExtremeSpeed
Shadow Hitmonlee lv 31 [Jump Kick]/Low Sweep/Mind Reader/Blaze Kick <Rock Head>
Shadow Staryu lv 30 [Thunder]/Surf/Aqua Ring/Extrasensory
Shadow Vulpix lv 30 [Extrasensory]/Flamethrower/Wisp/Dark Pulse
Shadow Sneasel lv 31 <PickUp> [Shadow Claw]/Ice Punch/Shadow Sneak/Knock Off (received a boost to its special attack)

(Pyrite Building)
Shadow Scizor lv 32 [CrossChop]/IronHead/BulletPunch/X-Scissor <Shed Skin>
Shadow Azumarill lv 32 [Superpower]/Waterfall/BellyDrum/Bounce
"If any of the above are KO'd you can find them Post-Credits in Pyrite Cave"
Shadow Altaria lv 35 [Flamethrower]/Dragonbreath/Roost/Airslash

(Pyrite Cave)
Shadow Medicham lv 32 [Mach Punch]/Extrasensory/Fake Out/Drain Punch
Shadow Camerupt lv 31 [Rock Slide]/Earth Power/Wisp/Heat Wave
Shadow Sableye lv 32 <Shield Dust> [Confuse Ray]Shadow Claw/Recover/Wisp
Shadow Mawile lv 34 [Earthquake]/IronHead/Superfang/SuckerPunch (received a boost to its special attack) <Huge Power>
Shadow Jirachi lv 35 [Doom Desire}/IronHead/Wish/Future Sight
"If Miror B's shadow is KO'd, you can find later at Realgam Tower/Deep Colosseum"

(Agate Village)
Shadow Nidoking lv 37 [Megahorn]/Poison Jab/Chargebeam/Drill Run
"If the above is KO'd you can find later at Cipher Lab/Snagem Hideout"

(Mt Battle)
Shadow Groudon lv 40 [Preciple Blades]/Earth Power/Bulk Up/Solarbeam
"If the above is KO'd you can find later at Realgam Tower/Deep Colosseum"

(The Under)
Shadow Tropius lv 41 <Thick Fat> [Dragon Pulse]/Woodhammer/Roost/Hurricane (received boost in all stats)
Shadow Kyogre lv 43 [Origin Pulse]/Surf/Calm Mind/Thunder
"If Venus's shadow is KO'd, you can find later at Realgam Tower/Deep Colosseum"
Shadow Houndoom lv 45 [Grassknot]/Flare Blitz/Nasty Plot/Crunch (recieved a boost to its attack)
Shadow Shiftry lv 41 <Insomina> [Airslash]/Woodhammer/Substitute/Knock Off
Shadow Ampharos lv 41 {Drain Punch]/Thunderpunch/Tail Glow/Dual Chop (received part Dragon typing and boost in attack power)
Shadow Gengar lv 44 <Intimidate> [Psychic]Shadow Ball/Toxic/Dark Pulse (recieved a boost in its attack)
"If any of the above is KO'd you can find later at Snagem Hideout"

(Cipher Lab)
Shadow Gyarados lv 41 [Fire Blast]Waterfall/Thunderwave/Bounce
Shadow Exploud lv 43 [Fire Blast]/Boomburst/Belly Drum/Bug Buzz
Shadow Glalie lv 44 <Inner Focus> [Head Smash]/Icicle Crash/Ice Shard/Iron Head
Shadow Milotic lv 41 <Natural Cure> [Reflect]/Surf/Aqua Ring/Moonlight
Shadow Flygon lv 46 (received a boost to special attack)
Shadow Zangoose lv 45 [Brick Break]/Slash/Swords Dance/Shadow Claw
Shadow Deoxys lv 45 [Extremespeed]Extrasensory/Barrier/Shadow Ball
"If any of the above (minus Deoxys) is KO'd you can find Post-Credits when you revisit the Lab"
"If Ein's shadow is KO'd, you can find later at Realgam Tower/Deep Colosseum"

(Realgam Tower)
Shadow Armaldo lv 47 <Swift Swim> [Irontail]Ancientpower/Fellstinger/X-scissor
Shadow Absol lv 47 <Intimidate> [Shadow Claw]/Sucker Punch/Taunt/Hurricane (slight boost to its sp attack)
Shadow Herracross (lol) lv 48 [Drill Run]/Megahorn/Rock Blast/Cross Chop
Shadow Slaking lv 55 [Earthquake]/Giga Impact/Sucker Punch/Focus Punch
"If any of the above is KO'd you can find Post-Credits in Cipher Lab or Snagem Hideout"

(Realgam Colosseum)
(you may want to train a bit for this part, or at least use the Ball Glitch, cause you have to do six battles in a row and four of them you dont heal at the start)
Shadow Salamence lv 52 [Outrage]/Dragon Claw/Flamethrower/Fly
Shadow Dragonite lv 55 [Outrage]/Aerial Ace/ExtremeSpeed/Dragon Claw <Shield Dust>
Shadow Tyranitar lv 54 (NOT Evice) [Earthquake]/Stone Edge/Dragon Dance/Crunch
Shadow Metagross lv 53 (NOT Nascour) [Bullet Punch]/Psychic/Light Screen/Meteor Mash
Shadow Mewtwo lv 55 [Thunderbolt]/Psychic/Recover/Shadow Ball
Shadow Rayquaza lv 60 (Evice;Final Boss) [Volt Tackle]/Fly/ExtremeSpeed/Draco Meteor

(Snagem Hideout)
Whichever Starter you didn't pick

(Revist the Shadow Pkmn Lab)
Whichever Starter you didn't pick

(Revisit the Snagem Hideout)
Shadow Latias lv 58 [Surf]/Psychic/Calm Mind/Dragon Pulse
Shadow Latios lv 58 [Hurricane]/Dragon Pulse/Bulk Up/Psychic

(Deep Colosseum)
Shadow Lugia lv 75 [Hydro Pump]/Hurricane/Disable/Psychic

(Outskirt Stand) Only appears if you capture all 47 prior Shadows
Shadow Mew lv 85 [Shadow Rush]*(yeah, seriously)/Psychic/Dark Void/Rainbow*
*Rainbow: Flying Type 100 Power-100 Accuracy 5 PP
*Shadow Rush: Typeless 90 Power 100 Accuracy -- PP

Nearly All TMs have been Altered
/All Buyable TMs are at The Under Mart/
/All exchangable TMs are at Mt. Battle/
List of New TMs
TM 01: Low Sweep (Pyrite R1)
TM 02: Hurricane (Deep R4)
TM 05: Discharge (Pyrite R3)
TM 06: Thunder Wave (Pyrite Story)
TM 07: Power-Up Punch (Pyrite R2)
TM 10: Psychic (buyable)
TM 11 Taunt (Phenac R2)
TM 12: Stone Edge (Deep R1)
TM 13: Surf (Pokecoupon exchange)
TM 14: Ice Beam (buyable)
TM 15: Thunderbolt (buyable)
TM 16: Flamethrower (buyable)
TM 17: Ironhead (buyable)
TM 18: Bulldoze (Phenac R1)
TM 20: Energy Ball (Buyable)
TM 22: Aerial Ace (phenac R4)
TM 23: Nasty Plot (Under R4)
TM 24: Draco Meteor (Pokecoupon exchange)
TM 25: Dark Pulse (buyable)
TM 27: Protect (PreGym Justy)
TM 29: Belly Drum (Pokecoupon exchange)
TM 31: Shadow Claw (Pyrite R4)
TM 32: Psycho Boost (Pokecoupon exchange)
TM 33: Scald (buyable)
TM 35: Heat Wave (Pokecoupon exchange)
TM 36: Icicle Crash (Under R2)
TM 37: (Will-O)Wisp (Under R1)
TM 38 Poison Jab (buyable)
TM 41: Helping Hand (Roller Boy Kaib Phenac City)
TM 44: Gunk Shot (Deep R3)
TM 45: X-Scissor (where you fight Venus the first time)
TM 47: Rock Slide (Mt. Battle Lobby after Dakim)
TM 48: Sucker Punch (Deep R2)
TM 49: Roost (Pyrite Cave)

All other TMs are either missing from the game or are unchanged.