Im from Pitt. area as well, used to be a paint contractor a few years back. I was always a fan of PPG and BM products. I never got into SW products, perhaps just a personal preference so dont let that sway your decision. If it were me, id definately suggest PPG's timeless. Only other thing I see that raises my brow is "5. Apply one coat of Exterior Solid Stain on all wood areas, Exterior Latex on Garage Doors and Tudor paneling and Exterior Oil on Front and rear doors" I do not believe in only 1 coat. You cant get the even coverage and durability with one heavy coat that you can with two lighter coats. Ive been out of the business for a while now but I believe two coats is even industry standard now. Other than that, looks good from what I can see.

The second guy might be using a scare tactic, hard to say. Replacement windows leave both the interior and exterior trim in tact unless there is actual wood rot (not chipped paint). installing a replacement window into the existing window frame and using a good interior and exterior sealant along with foam insulation is tried and true method we all use. Of course, if there is existing wood exterior casing, we cap with aluminum. what brand of window was quoted?

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.

IMO you wait until you do the rest and then see what is needed . You do not have any space for proper shutters IMO so no to them. Iwould like to see the front of the house since the back and front should have some connection to each other.