For a 998 the Maniflow 3-into-1 manifold with a single box is fine. Pipe diameter should be 1.625" diameter, as the original Mini Cooper 998.
On the subject ot twin carbs, my personal feeling is that a pair of HS2's on a 998 with a well-flowed head and a good exhaust will be more efficient than a single 1.5" carb. The inlet manifold for the twins needs to be cleaned up with the internal steps and sharp edges removed. I can't quantify the advantage, but better mid-range seems likely as well as more top-end power. Two individual chokes feeding two inlet tracts seems logical, but the original BMC inlet manifold might be the weak link. There are better inlet manifolds for twins, or the BMC one can be improved considerably. I found an old 'Torquemaster' alloy inlet manifold recently with a pair of H4's in need of rebuilding on it. I might fit this to my 1990 Cooper 1330 road-rally car which currently has an HIF44.