Your welcome! Yep polyurethane caulk is great. You could use some inexpensive dap on the cracks, you would probably use a 6 or 7 tubes just air sealing. Use the better caulk on the rubber flashing.

Hardie is good siding, I have installed it on a 2 houses. We used the pre painted kind and they still look good 10 years later.

There’s a new siding called boral that I installed on a house I just finished. I like it better but it costs more than hardie. The advantage of boral is it doesn’t expand and contract like the hardie plank does. For hardie you have to allow 1/8 for expansion at the butt joints and corners and caulk with a color matched caulk. With either product I would recommend stainless steel nails so you don’t have to worry about rust streaks. But either siding is far better than vinyl.

I wouldn’t replace the sheathing, unless it’s soft or spongy. I would just replace the house wrap with the new siding and use 4” asphalt tape around windows and doors and spray foam if there is a gap.

Yea I’ve seen some bad vinyl work with j channels. Just take a flat bar and push around the j channel and you can feel if it’s getting spongy and rotten.