A crude shortcut, to enable you to get all tracks onto one midi file is as follows:
Using MidiSwing, is to open the file; Command A (copy all); Menu - File - New SFM0 – Command V (paste all) then readjust the tempo.
There are much finer 'performances of William Tell freely available on-line.
There are very good and not very good midis available from the internet. You can do a lot better than that midi.
I know the site you mention. I subscribe to it. There some wonderful performances on it from reproducing piano rolls and some from skilled living pianists. Look for the yellow 'Historic Performances"' and "Live Quality". Please don't waste your time on poor quality sequences when there is so many great 'live' performances available.
Many midi files, like the one you mention, have been scanned from scores and converted to midi. These are possibly useful for study purposes but they are produced by a computer, not a pianist and, like the little gift cards that play tunes when you open them, they are mechanical, not musical. Your piano is capable of astonishing concert performance realism and you really can't get that realism from 'sequenced' midis.
Go to http://yamahaden.com/midi-files or search for Spencer Chase or Terry Smythe archives ; Search 'midi' with any of the following names: Oguri; Ozaki; Tryon; Doug McKenzie; Lubetsky; Carter. Finley; Bill Edwards; Fracalanza; Giulimondi; Lloyd; Bob Mace, all of whom have freely available midis of outstanding pianism.
Alternately, if you are serious about quality reproduction, then buy some files, as I have, in bulk from https://www.petersmidi.com/
Good luck,