I'm working on a project where we have a large number of MIDI files and want to combine them into new files with more notes. We want to combine them both in parallel, so that two combined files play at the same time and put their sounds on different tracks, and in series, so that one file plays its sequence, and then on the measure afterwards, the next MIDI file starts playing. Are there any tools or techniques to accomplish this?
You can use a DAW such as Cubase (or any other similar). This has functions to import your MIDI files which allow you to split the embedded tracks (based on channels).
You will then get the note data spread to multiple tracks and can move them around as any clip. Assign a sound to the track and you're good to go.
You can finally export your project as a new MIDI file.