Assuming the 140 is the same general construction idea as my 120 FHC, the 2443 bar should be under the metal floor panel, and the 2359 flat head screws hold it up, and the holes in the floor and bar are countersunk so the screws will sit down in it. They do not significantly weaken the floor, as there is no force trying to pull them out. The NS525/12H screws go through the countersunk holes in the 2440 runner and straight holes in the 2445 wedge into the 2443 bar, in which there should be non-countersunk threaded holes for them.
The only questionable thing is that you say some of your holes in the 2443 bar are not tapped. I think they should be. Further investigation is indicated.