"For the backer rod, do you simply caulk that in place or is there another form of attachment method that I should use first? " It should be large enough to require forcing into place before covering with caulk. About 505 wider than the gap seems to work well. If you need to you can even split the rod using a sharp utility knife. Uneven gaps can be a PITA to fill. the backer is just there as a base for the caulk, so using separate pieces as a long gap varies in width is not a problem (except for installing it). if any gaps remaining are small enough, caulk will not get through them badly anyway. Tiny gaps at mortar joints (less than 1/8 inch or so) can usually be tolerated. Part depends on how thick (viscosity wise) the caulk you are using is. A smooth caulk surface will look better up close, and if you apply it carefully ad too it smooth can look acceptable. You get some relief on second story work since no one normally can get close enough to see it well (but around a front door or ground level window looking onto the front steps needs to look nicer).

I don't know if any of you are still around to answer me on this. I too have windows that have gone in and the sill pans didn't get put in beforehand. I also live in low rain Los Angeles. The 40 Fleetwood windows installed even had a custom sill pan included but they didn't get installed. Fleetwood says the lack of sill pan voids the warranty. On top of that my contractor DID NOT prep the sill at all. The bituthene does not wrap over the sill at all, it's just placed around the outside of the window openings. The windows are installed but look really sealed well now with a layers of bituthene over the window flange and he used lots of caulking. He stands by how they are installed and will put it in writing that they will not leak. He says he usually tosses out sill pans! He says his insurance will cover it for 10 years as well. To just add context, I had a garage fire and the property is currently gutted because of smoke damage. 30% of the exterior stucco has been taken off and new waterproof paper will be installed and the browncoat will be replaced then the whole building will be wrapped with a stucco mesh covering to prevent cracking and disguised the stucco damage around the new windows. Apparently the wrap adds some water resistance as well. The roof is being replaced as well. The new electrical is going in so I have time to correct the windows if you guys say I need to do it. It will cost me about $10,000 to reset these windows. Would you do it?

Love your house! I second to not remove the shutters as they balance out the narrowness of the windows. You have a big, solid looking house and without them the proportions of the windows seem to be a bit off. They also give a visual break to the expanse of walls unless you could add some wide trim around the windows. Your house has a commanding presence and I think it would look stunning in a darker color which would also stand out from all the other houses in your neighborhood. I also would take a sample of your flagstone and get it color matched when it is wet. Below is just an example. Wonder if someone could photoshop a dark color with white shutters just to give you a comparison to the light colors above and see if you would like it.

I think I have the same siding as you - it looks like Hardi Board. Those nail holes look wrong to me. If those are on every piece of siding then the original installer didn't know what they were doing. Except in special situations, the nails should be covered by the piece of siding above. There should not be nails down low on the siding. Since those holes should not be there, I would think that filling them would be an extra step. FWIW my neighbor has the same siding and the installer caulked the seams between the boards - the vertical seams. It looks horrible because the caulk is a different texture than the siding so it sticks out. Caulking those holes would probably give you the same result - strange shiny dots on your siding. Having said that, giving water a path into the siding is not good either. But if the house is several years old and that has not been a problem, you are probably fine. On the soffit - I would have someone finish that area with an appropriate soffit material that will accept paint well and hide the 2x4s and plywood that are there now. No amount of paint is going to make that look good.