I found that the technique used for hacking SNES palettes described here also works on PSX CLUTs.

However, sometimes I find around 50 or even over 100 matches for a color I want to replace, and entering the same RGB values into SNESPal over 100 times is time consuming.

Is there another way or an alternate program that I can use to find and replace all instances of a color all at once instead of changing each instance one at a time?

If you're editing a TIM's CLUT, then why not extract the TIM and modify its CLUT directly? You're not looking for the values on the ISO, are you?

If I recall correctly, the CLUT is near the start of the TIM file.