The program you use to record SHOULDN'T matter. If you record your parts as Wave files, they'll play in any program. If you record them as MIDI, ditto, but the sound or effect you use obviously won't be the exact same. As for the guide we all use, there's no perfect solution. I used a MIDI for "Starship Trooper" but on the end product my stuff was off-time (sorry Ed!!) because MIDI can slow down or speed up slightly during the recording and/or playback process. The reason we didn't go with CDs is because they, too, don't always play at the EXACT same speed, depending on the CD player (and presumably depending on the album you're using as a reference; "Trooper" is on at least eight different CDs overall).
So, there's no perfect solution, alas... but we can still make a go of it!
As for the issue of which song... we seem to have so many guitarists here, why don't we do 'splinter' projects? Maybe break it into groups. That would also be easier for whoever mixes it (me, Ed, who else?) because we don't have to give ten different guitar players a little 'solo' in the span of one song!
Even if it IS a Yes song! Some want to do "To Be Over", some want to do "Changes" (I know I'd be up for both, but being the Rabinite that I am, I'd especially have fun with the latter), so pick your favorite and work with it!