Did a little searching for this, and thankfully the MediaFire links are still up.
E-101 Beta Mark II: http://www.mediafire.com/download/ks7aevwlb0m9ea6/MG-BetaMKII.rar
Egg Carrier (The Ocean): http://www.mediafire.com/download/87m00og4xba57d0/Egg_Carrier.rar
Both the character and stage were made by MGSSJ2.
Also here's a handful of stages made by Magma Dragoon MK-II.
Hidden Palace (there's 2 versions of this stage but both of them are based off of S&K)
Mystic Ruins (again, 2 versions)
Doomsday Zone (could probably be put in misc. as it's moreso an original stage using the name rather than the actual Doomsday Zone)
Tails' Training Shuttle (Misc.)
Emerald Dimension (Misc.) (Once again, 2 versions; specifically Mystic Ruins X and Emerald Dimension X are the more recent versions of said stages)
Metallic Madness Ruins
Ruins of Tera Zone (Misc.)
Mushroom Hill
Palmtree Panic Arena
Death Egg Throne Room
Sky Sanctuary