Hi Frank; It’s a wonderful project – kudos!

I was around back in those days and have made that house and others that use the same ‘stacked-molding and connectors’ technique, and I offer these suggestions.

Paint everything (that will be painted*) one-coat, and sand down to the wood before beginning construction. The quality of the final paint job is 100% dependent on the quality of the sanding after the first coat, and it is impossible to do a good sanding job after assembly. *do not paint the outside of the roofs, the foundation parts until they are pre-assembled, the insides of the connector’s grooves or the lips and grooves of the clapboard pieces (if paint gets on them here and there, it’s no big deal, but as a global intention, that’s not where you want the wood sealed). Do not paint inside the window parts’ grooves. Painting the second coat is a back-and-forth process of painting and assembly. In most cases it is best to assemble and then paint the assembly from a strength point of view. Glue won’t stick to a second-coated part very well, so things that require strength should either be painted after assembly, or should be marked and scraped for gluing to get the second-coat of paint out of the way for some glue contact inside the joint (where the scraping will be invisible). I often mark a joint, paint to just cover the mark, and then glue so the paint is perfect (with the transition hidden in the joint – a level of perfection impossible to achieve with masking for paint color separation) and the glue is wood-to-wood. So, test ahead and make decisions along the way when to do the painting.

The wall sections WILL expand and shrink seasonally with changes in humidity. You can either accommodate that or resolve to be at peace when the walls split or separate as they shrink. The two techniques I have used to accommodate that movement are:

1) Glue the walls together thoroughly, but glue them into the connectors only at the bottom 2”. Glue the windows into the cutouts only at the bottom 1”. When the walls are glued to the floors, only glue the walls at the bottoms, not at the tops. This allows the walls to shrink away from the top which is partly hidden by the nosing. On the inside, gluing a strip of ¼ x ½ to the ceiling on the inside of each wall (but not to the wall), and to the connectors at each end to reinforce the joint at the top without interfering with the wall’s ability to shrink away. The downside of this technique is that the next higher floor is only connected at the tops of the connectors and by the Dividers. If the house is to be moved around much it makes it vulnerable to breakage.

Or:
2) When you paint the clapboard sections, paint the tongue of each piece thoroughly as you paint the rest of each piece. Paint the clapboard pieces with two coats sanded between coats or more if needed (don’t paint the ends). Glue the wall sections together with small amounts of non-structural glue like Quick-Grip or Magna-Tac, and glue them into the Connectors with a fully structural glue (like Aleene’s Tacky Glue). Glue the tops and the bottoms to the floors (scraping for a good joint or mark&paint as explained above). The downside of this technique is that as the walls shrink each section will separate at the tongue-and-groove, and this separation will be visible, suggesting to the owner that they ought to fill the “cracks” on the inside to make them smooth. That fill will literally tear the house apart and it will collapse. To prevent that, interior finishing (painting, wallpapering) should be done on card stock and loosely glued to the insides of the walls, so down the road no-one will try to ‘fix’ the walls. The other liability is that assembly really needs to be reserved for the humid times of the year. This is not a winter-time technique in the north country (when central heat makes the inside humidity really, really dry, and wood is shrunk to its lowest size of the year). The separations between the clapboard pieces will be visible but is necessary for the wood to be able to move freely. If the individual pieces are fully painted, what shows is an extra wide shadow every 2½”, and using this techniques means being at peace with that amount of visibility during the dry part of the year.

I hope this boat-load of reflections doesn’t put you off, though. This is a wonderful project and, with some thought to the natural behavior of wood, it will be an heirloom build.
Best wishes