Jimmy you probably know this but there are many variables. Here are three I can think of:
1) The engine mounts (the brand and type of isolation mounts) and shims if installed, affects how engine is hanging and alignment in vertical and horizontal planes.
2) The fit and alignment of the cowl relative to airframe and engine is a big factor, totally on builders control, so expect variation.
3) How the builder fits the baffles affect the plenum to cowl alignment, but should be least of the variables but still a factor.
If you use a given RV for test fit, it may be at one edge of the tolerance envelope of variables listed above and some I can't think of. The customers plane may be quite different from your test fit plane you based your product on, and the plenum will not align well with cowl. In other words you try your plenum on a plane and it does not fit well it could be their plane is off not your product.
Engine is a living beast shaking like a wet dog, moving up & down, side & side. Flex coupling between cowl and plenum distance is short. You need good alignment to give room for the engine to move with minimum strain on the flex couple, cowl and plenum.
Many DIY plenums use the van baffle kit, separate roof to the dog house (aluminum or fiberglass) and individual inlets usually molded out of fiberglass, mechanically fastened in. The inlets are formed plugs made in-place for custom fit on that setup. Consider separate parts to allow more flexibility. Mechanical fasteners allow easier adjustment to move or shim the inlets, verses one piece fixed and locked in.
If I were doing it from scratch today I would have the ENGINE, baffle fitted temporarily then fit Cowl, allowing adjustments of cowl, plenum and engine to get best fit before nailing it all down.
I know in the past as the OP of this thread suggests many people had to cut and re-glass the planum to get it to fit. If I am out lunch and wrong just ignore my comment. I went with the DIY plenum because it seemed easier and would take care of any variations I had, i.e., a custom fit.