Yes, Squiffy, you have found the problem!
As far as the cockpit/fuselage assembly fitting the lower wing, it is indeed a bear. On my first Pup, which was for me, as well, a first foray into 1/32, I ended up grinding off a good bit of the edges of the cockpit floor. It was positively Neanderthal-istic. On the current build, I removed the semi circular raised portions, as advised, and went further by scraping a good bit off the mating section of the lower wing.
The other thing I learned on the first build was to pre-drill all the rigging holes on the tabs attached to the struts. I am sure this was just a rooky oversight on my part but I've gone over the present build to make sure all the rigging attachment points are really clear before I assemble all the sub-assemblies.
Also, there was something funky about the way the forward cabane struts attached. I think it's that if they are not set exactly right the cowling won't sit perfectly.
Other than those particular issue, it was pretty smooth sailing and a real joy to build. This second one is going together like a hot knife through butter.
Cheers from NYC,
Michael