Hi Gareth, I think that instead of trying to loft the fuselage and intake both at the same time, you'll probably want to do the fuselage as one big unbroken surface, then use Trim to cut out a section of it and work on forming the air intake as a separate piece from it, possibly using Blend to connect it smoothly to the main fuselage.

Check out Mike Maynard's tutorial on "Transitional Recessed surfaces" here which is kind of similar to what you're trying to do I think:
http://moi3d.com/forum/index.php?webtag=MOI&msg=4880.1

That is generally a pretty difficult kind of shape that you're trying to tackle there. But often times an abrupt transition can be better modeled as an initially bigger extended surface and then cutting away some material from that rather than trying to directly surface it all in one big single loft. Sometimes a big loft can work but it's tricky because the more sections you try to use often times applies more sort of "pressure" on to the forum and can make for tortured surfaces.

- Michael