Morning Dave........just a few observations
1. you have a water line for the original 1890 Drawings
[even without CAD facilities it is clear our forefathers had great skills in lofting and ship Drawing skills]
2. many vertical or and horizontal references have imported the Drawings into CAD. Apart from the waterline, many of these line references will continue to confuse you
3. you also mention that you have contacted a Ship Repairer of vessels of similar vintage....and their response will hopefully confirm a few basic building principals
My best guess for construction are as follows
a. yes the keel would have been blocked and chocked so the hull frames would have been in true vertical alignment during the build
b. the boiler bed would also have been at 90 degrees to the vertical........[two water gauges or pipes I have highlighted would require by design to be truly vertical when the vessel was at her waterline]
c. the vertical axis of the engine to be at 90 degrees to the angle lay of the propeller shaft
d. when the vessel was at her waterline, deck and roof levels would be angled to the stern, with doors at that same angle off the vertical
There are also many publications of Wooden Built vessels of similar displacement/design & vintage and would be a valued read they would also allay any fears of the correct method of construction
A number of compromises will be needed with a model build, however a reasonably true model can be constructed when the intention is for display. Many models with one side framed but unplanked beautifully expose the scale internals of both build and machinery
A very interesting project
....please keep us posted with your progress
Derek