I agree with Emily_Mb. The two most essential words in your OP are "small" and "shaker". So, I would do taller cabinets, either 39" or 42", no soffit, and with a simple molding that fills it up to the ceiling. You say your kitchen is small. I think soffits are nice when you have a large kitchen, but a waste of precious space in a small kitchen. Also, I think you can never have too much storage in a kitchen, and 36" cabs won't give you a whole lot, especially for taller items like wine glasses or cereal boxes. You say your kitchen is Shaker. Huge moldings are not suited to the simple Shaker style, and (just MHO!) I think they are too fussy for a kitchen, and more suited for a library or den. If anyone says that tall cabinets aren't good because the top shelves are too high, well, I don't agree. First, the top shelves are great for storage of infrequently used items (holiday dishes, light bulbs, etc.). Second, unless you're tall, you'd need a stepstool for the top shelves of 36" cabinets anyway, so needing a stepstool for a 39" or 42" doesn't change anything.

Here is the link to the stain that Patina Farm uses for their projects. Are you sure you want to use pine? Maybe consider cedar for the ceilings https://www.superdeck.com/ https://www.superdeck.com/product/semi-transparent-stain-waterborne-2400/

If your cabinets were built from scratch and built in place, they may be mounted down from the ceiling. While that wont affect the ones you want to remove, it could affect the ones on the opposite wall. At my last house, that was the case, and the soffits had to be left, since all my uppers were mounted and attached from the ceiling. You can still remove the ones you want to remove, but, may not be able to remove the rest of them. Take it apart and remove the facing lumber, so you can see behind it. At one time, that facing lumber was probably viewable all the time. Someone then wallpapered it, and now it looks like that wallpaper was painted over. The wood you are seeing is what was there originally.

Lovely home. I'll let an architect/designer chime in on the most appropriate soffit direction to take, though I would say in the long run, lose the vinyl. For windows: I almost always advise keeping old windows. It sounds like some are in disrepair - unless they are completely rotted or something, they should be able to restored to complete function. There are companies that specialize exclusively in historic windows, though some contractors also have the skills (if you're fairly handy, you could figure it out too). As far as lead exposure goes, the concern isn't so much lead existing in your house as much as it becoming airborne. If the paint is in good condition, that would only happen if you were scraping/sanding paint or some other demolition. If you're still concerned though, a good prime and paint will give you an extra layer of security.