Siding- flashing installation

Following Hurricane Rita repairs in the Beaumont area, I want to replace my wood siding with Hardy plank (fiber cement) siding. The siding I will be replacing is on the second floor exterior wall. The roof was replaced after the storm, and I cannot tell until I strip off the old wood how the flashing is installed now. I do not know if the roofer tucked the flashing under the shingle.

My questions is:

After I remove the existing wood siding, do I install the flashing under the new Hardy plank on the wall, then lap the flashing over the shingle? I don't know whether to install the flashing under or on top of the shingle. However I do it - I will seal it with some kind of roofing cement. What type of roffing cement would be recommended?

I got a couple of prices for this work, but neither contractor had ever done this work before, and for 1000 ft2 area of wall - they wanted $ 10,000.00
( material is $ 1,800 approx.)

I do not mind paying for services, but I will not be ripped off.

I've got scaffolds, a miter saw with carbide blade, cool weather, and protractor- I just do not know about the flashing installation.

Thanks in advance for the help.