It's been so long ago, I can't remember exactly how I ripped this but would have been either:

1) Loading the ROM via TileMole-ster set towards 4bpp linear if not already set, find the tiles, may have to adjust the offsets with + and -, export them and arrange them using GraphicsGale. Success rate is lower than you would think due to compression.
2) Making a savestate from an emulator (would have been either Kega Fusion, Gens GS or GensKMod) then loading it in TileMole-ster, same as Step 1. No compression issues but may have to do this many times.
3) Most likely using a version of GensKMod that gives a pink background, removed layers and captured as in took print screens. This is because it's common for MD games to have a black background while the sprites also use black. The settings would have been native resolution without any filters or stretching (since some MD games do not use 320x224 video mode). Nowadays would have used GenesisPlusGX via BizHawk to do this due to having the same features plus correct or close to correct palette and the tile viewer can also be made pink (even though something that I noticed, it only affects the first row and sometimes it can be the other rows that do this).

In all cases the palette had to be corrected because older emulators and tools didn't have the right palette. Don't have to now but had a cheat sheet for the values.

I want to know how Yawackhary ripped the sprites for Pikachu and the bosses, because I've been meaning to rip the enemies but everything I've tried didn't work

https://www.youtube.com/watch?v=EbPw6-Z2pkU
I found a playthrough of the snes version of this game with the other colors of the bosses

*Obligatory Jontron reference*