It is probably better to work with a conventional after market sun roof installer.
My guess is that the only Honda part that you can readily buy is the glass. That means you have to still worry about cutting the hole in the roof, rolling the edges, fabricating the frame that the glass beds in. In addition you have to install some sort of water drain - Honda uses 4 tubes that run under the interior trim. And don't forget about modifying the ceiling liner.
Awful lot of work for the do-it-yourself type, especially if this is your first skylight. If it isn't done right you'll get wind whistles, rain leaks, and ugly appearance (inside and out).