The 2/3 1/3 rule would have 36" cabinets have 18" cabinets on top. And you never want a light rail that thick if it's got to be above the 18" clearance. Typically, the bottom of the cabinet is 18" above the counter, and the light rail takes the clearance down to 17" to 16 1/2".

With 9'1" ceilings, what I'd personally do would be 33"+ 15" (with the bottom alignment at 54") plus a stacked 7" molding for the rest of the height. And put on the light rail after inspection. As long as your hood is wider than the cooktop it covers by at least 6", it's not a fire hazard at all.

Thank you hollysprings for all your help and suggestions. Having everything above the 18" including the valance is what's really throwing it all off for me.

The annoying part is the builder has 39" cabinets standard and if I reduce their height I don't receive any credit, and if I increase the stacked uppers height from 12" to even by an inch I pay more even though in reality its the same amount of wood on the wall. Frustrating. Lol.

Another thing I'm wondering about is the custom wood hood, I now have a 30" range and the wood hood is 37" wide, in the new build I have a 36" range and she has a 39" wide wood hood in the plans. So that's not giving the 3" clearance on each side, is that correct?
I'm also going to get KD to do a perspective of your suggestion and see how that looks.

Here are the codes it all needs to follow and I'm wondering also if I keep the bottom of cabinets at 54" if I can still add the under cabinet lighting before inspection and add the light valance after. I'm going to call the cabinet designer tomorrow as well as the builder.

Here is a link that might be useful: Clearance codes