It's actually not that difficult. First step is to get yourself an editing program. A free one like Audacity will do.
The source for my edit was the Nick Davis remix, Ray Wilson's Live With The Berlin Symphony In Poland and one of the bootlegs from the Calling All Stations tour (either Poland or Mannheim, I'm not sure). Luckily, the 'live' performances were at the same tempo as the studio version, although the version on Ray's album was in a different key (changing the key wasn't a problem as I wasn't using a section with vocals in it).
Ray's version of the song has the guitar solo occur immediately after the bridge and I thought that worked well so I followed suit. So, it's bridge, solo from the Ray album and then solo from the Genesis concert and then back into the studio version.
Getting the solo to the point where it integrated seamlessly with the sound of the studio cut involved a lot of fiddling with EQ, compression and all that jazz but I didn't mind. My fan-edits are a labour of love for me (not for my wife, though; she hates them! "Can't we just listen to the album as it was intended?" she will often say.) and I'll work on them for as long as it takes. Many's the time when I've committed something to disc only to decide, after a few listens, that I need to go back and do it again.