Lovely Doll you are showing here, and I look forward to the restoration which will bring her into her prime I've no doubt!
Doll #354 seems correct, but there is some ambiguity concerning the features that raises questions as to whether it is a 354/2 or 3.
The 354/2 is not shown as having the faux governor, while the 354/3 does, however, the 354/3 does have a water drain tap while the 354/2 does not, and I don't see one on your engine either. It would not be strange at all for a minor feature like the faux governor to be missed in the catalog or added to an engine without the catalog image being updated. Also, you are correct that your chimney is not correct, but it doesn't noticeably detract unless you really know what you are looking at, so I'd keep it until (if) you ever find a correct stack!
It seems each of the different sizes offered progressively larger flywheels and taller boilers, so that is likely the best measure to determine actual model number.
See the chart here:
http://www.ventix-pages.de/doll/D-Dampf/D-Hauptgruppen/D-Vertikal/D-354/d-354.html