Use the "Lunar IPS (LIPS) - IPS Patch Utility" to use the patches.

The romzip for Ultimate Mortal Kombat 3 + Beta II should be named umk3p.zip and the romfiles inside should be named
as below:

64-BIT:
  u54_umk3plus.u54 (will need to name your IPS patch files this name)
  u63_umk3plus.u63 (will need to name your IPS patch files this name)
  l2.0_mortal_kombat_3_u2_umk3plus.u2 (will need to name your IPS patch files this name)
  l1_mortal_kombat_3_u3_music_spch.u3
  l1_mortal_kombat_3_u4_music_spch.u4
  l1_mortal_kombat_3_u5_music_spch.u5
  l1_mortal_kombat_3_u133_game_rom.u133
  l1_mortal_kombat_3_u132_game_rom.u132
  l1_mortal_kombat_3_u131_game_rom.u131
  l1_mortal_kombat_3_u130_game_rom.u130
  l1_mortal_kombat_3_u129_game_rom.u129
  l1_mortal_kombat_3_u128_game_rom.u128
  l1_mortal_kombat_3_u127_game_rom.u127
  l1_mortal_kombat_3_u126_game_rom.u126
  l1_mortal_kombat_3_u125_game_rom.u125
  l1_mortal_kombat_3_u124_game_rom.u124
  l1_mortal_kombat_3_u123_game_rom.u123
  l1_mortal_kombat_3_u122_game_rom.u122
  umk-u121.bin
  umk-u120.bin
  umk-u119.bin
  umk-u118.bin
  umk3p-u117.bin
  umk3p-u116.bin
  umk3p-u115.bin
  umk3p-u114.bin
  umk-u113.bin
  umk-u112.bin
  umk-u111.bin
  umk-u110.bin

32-BIT:
  umk3plusu54.bin (will need to name your IPS patch files this name)
  umk3plusu63.bin (will need to name your IPS patch files this name)
  umk3plus-u2.bin (will need to name your IPS patch files this name)
  umk3-u3.bin
  umk3-u4.bin
  umk3-u5.bin
  umk-u133.bin
  umk-u132.bin
  umk-u131.bin
  umk-u130.bin
  umk-u129.bin
  umk-u128.bin
  umk-u127.bin
  umk-u126.bin
  umk-u125.bin
  umk-u124.bin
  umk-u123.bin
  umk-u122.bin
  umk-u121.bin
  umk-u120.bin
  umk-u119.bin
  umk-u118.bin
  umk3plus-u117.bin
  umk3plus-u116.bin
  umk3plus-u115.bin
  umk3plus-u114.bin
  umk-u113.bin
  umk-u112.bin
  umk-u111.bin
  umk-u110.bin