The most effective way to get MIDI data from these files is by using specialized "ripping" tools that understand the GBA's internal sound drivers. 1. VGMTrans (Recommended)
When you play a MINIGSF file in a player like foobar2000 (with the GSF plugin) or Winamp, your computer emulates the GBA’s audio processor in real-time. It runs the game’s audio driver, feeds it the sequence data, and outputs a digital audio stream. minigsf to midi