Please excuse me, maybe I did not directly answer your questions, please let me clairify my remarks.
1) If your whole site is in the 100 year flood zone, then all six buildings are in the 100 year flood zone. If the original flood study is not available, then I would simply overlay the contours on the fema map and see where the 100 year flood limits are. At each building, the furtherst upstream building point perpandicular to your natural channel flow path, I would determine the 100 year base flood by interpolation. I would conservatively interpolate to minimize flood damage. Please remember to mitigate all fill placed within the 100 year flood plain.
2) If you mean desire to place two buildings in the 25 year flood plain or flow channel, forget it. The 25 year flow channel should not be disturbed, if you disturb it then you must remodel the system. (I do not really understand how your whole site can be in the flood zone but only 2 building really affected by the water, unless the 2 building are in some lower flood zone, like the 25 year. Unless, the whole site is in the 500 year flood zone and 2 buildings are in the 100 year flood zone.)
3) Please see my previous remarks(11/27) about grading, 18" is no big deal. Remember, ADA pedestrian paths may be under 5% maximum slope without a ramp and under 2% maximum slope is considered flat. DO NOT FIGHT YOUR SITE. Accept it and do your best within its limitations. Remember, if you cheat, then you may pay for it, but if you do it right, then it is a just development cost paid by the owner.
4) Consider using catch basins to make grading easier. Consider alternatives for lowering the local flow line, like putting all the building on the same side of the roadway and collecting the water on the other side or using a 20' wide grassed median to collect the runoff, etc.
5) If the 100 year flood zones have been determined, then the 100 year Base Flood Elevations are determined. They may be given implicitly in a graphic format by the FEMA flood map (See comment #1). If you have some non-FEMA flood map. then you need to determine the flood zone via a FEMA acceptable methodology. (See previous 12/11 comments, #3-#4)
6) You only need an acceptable method to determine the BFE. There are many acceptable methods but no single method may satisfy everyone. You only need to satisfy the stormwater reviewer and follow accepted practice. See comment #5.
7) I assume that you are working under a PE. You may need to conference with him. Also, your problem may not be unique. Speak to the stormwater and ADA reviewers. Ask to see simmilar projects. Ask a contractor how he would solve your problem.
8) An old boss once told me - "Just do it, do not play with it." Start from the easy and work to the hard.
Best of Luck...... Clifford H Laubstein
FL Certified PE #58662