A midi file is essentially a "music score" which does not store actual music, but rather, the note to be played at time X at a certain tempo in track Y. Therefore, converting a mp3 into a midi would be like converting music to written instructions; a machine is not very effective at doing so, as it takes a good amount of time and effort for a human to do, as it requires the distinguishing of different instruments and pitches with a certain rhythm.
In all honesty, there are no programs that can turn any audio file into a pleasant, workable midi. For the best results, a human would have to create the midi file based off of what they hear throughout the audio.
Using Anvil Studio, you can mark the loop end and start by adding a new cue and labeling the start "[" and the end "]".
This question is oddly vague and confusing. I suppose you would be continuously working on it throughout? If you want to edit the midi, do it before you use mid2agb.exe.
It has to be a valid midi file for midi2gba to work. The only program of particular interest and use is the "mid2agb.exe," which produces a .s file which can be inserted into the ROM using sappy.