it sounds like PakkIso is what you need. You could probably do everything manually but it sounds like Pakkiso will do it automatically, so there's no need.
Also, the .ape files are probably Monkey's Audio, which is a lossless audio codec (I'm presuming they used it because of that reason). Bin.ecm is an ISO image (in this case it sounds like JUST the data track) that has been put through Neill Corlett's
ECM program. ECM tends to make ISO images compress better...the process is easily reversible, so it's kind of a win win situation.