I decided to install the Aristo-Craft, ART-29706, floor assembly with its shallow bolsters starting with my Reefer cars, particularly the PFE cars. This makes the cars closer to the trucks and less overall height from the rail head, thus more realistic.
One BIG revelation I came upon whist doing this task was discovering that all my cars had their original floors installed backwards! That is - the AIR tank end should be placed closest to the NON brake wheel bulkhead.
I had looked in my books to verify the proper placement of the air brake hardware with respect to the car's brake wheel bulkhead.
Of particular importance is the book,
"Pacific Fruit Express PFE", published by Signature Press, ISBN 1-930013-03-5,
pages 168 - 170 inclusive of photographs and an engineering fold out drawing of the PFE car between pages 432 and 433.
The book pictures and drawing clearly show that the floor's large AIR tank should be closest to the car's NON brake wheel bulkhead whilst the smaller brake piston cylinder should be closest to the brake wheel bulkhead. This orientation is unlike virtually all Aristo-Craft Reefers, Box cars, and Stock cars that I have examined.
In this regard, it is very possible that the Aristo factory has been assembling all these type cars incorrectly (not just the reefers) for more than a decade!!
Shown below is the Aristo-Craft PFE reefer car with its factory assembled wrongly oriented floor with respect to brake wheel bulkhead: 
PFE reefer with its brake apparatus parts shown. (Note the location of the air tank with respect to the brake wheel is indicative of this floor being installed in the wrong direction.)
Now to proceed with the new floor installation:
When installing the new lowered floor, I oriented it properly. (There is no "key" in the car or floor that requires its installation in a given direction, so all you have to do is turn it around 180 degrees.)
Aristo-Craft 40 foot freight car type Old and New lowered floor bolster comparison (the one below is the new floor and has the shallow type bolster): 
PFE reefer car with floor parts removed (Also shown is the side view of the newer floor next to and below the original floor):
The Aristo lowered floor assembly, ART-29706, may or may not include new brake linkage and air tank parts. When salvaging such parts from the original floor, I found removing the plastic brake linkage hardware to vary from prying it up with a flat blade screwdriver - from an apparent press fit - to having to break off the little unseen fasteners while prying it. This is because the factory appears to use glue on a random basis! When installing the linkage on the new floor, I used CA glued as needed.
PFE reefer with new lowered floor and former hardware removed from the original floor: 
PFE reefer floor showing holes drilled by factory in its side to accommodate the wire foot stirrup:
PFE reefer with new floor (once installed) must be drilled with a small drill bit to allow for installation of the wire foot stirrup. I used a pin vise for this operation.
The PFE reefer requires 6 long screws to mount its floor to the car's body. (It is helpful to open the side doors and ice hatches to see how the long screws are aligned with the small plastic bosses within the car body): 
The PFE reefer's new lowered floor requires use of a flat head bolster screw rather than the pan head screws to avoid interference with the truck side frame. I used a 4-40, 5/16 inch long Philips black oxide type screw installed in the bolster - see example where the Xacto knife is pointed:
The new lowered floor has one different mount location for the transplanted, former brake linkage.
(To avoid possible wheel flange rubbing when operating the car on curve tracks, the shown unattached link projection should be cut slightly shorter or glued down on the floor post.) 
Before transplanting and installing the truck assemblies to the new floor, check the trucks' brake shoes projections:
To avoid possible derailments, the Battendorf truck type brake shoes of the older production run cars must be trimmed to prevent rubbing on the rails, hitting rail joints, etc. when Aristo metal wheels are retrofitted. (The Aristo, ART-29111, replacement metal wheels are slightly smaller in diameter than the original plastic wheels.) I used a file to slightly trim the projecting shoes. Alternatively, you can use a cutter to snip off the projections.
Aristo-Craft PFE reefer cars compared. The lowered floor version car shown to the right with the most noticeable difference being the spacing between the truck and floor. 
A more distant view:
Aristo-Craft PFE reefer cars showing perspective view with the car in the foreground being the lowered one:
The newer production run Aristo-Craft 40 foot cars include the new lowered floor assembly - albeit installed with the wrong orientation as my CN reefer was.
I noticed these cars have a tendency to wobble too much from side to side. See the picture below of Aristo-Craft CN reefer with truck removed showing metal washer on the car's floor bolster. (The cars with the older floors do not have this washer installed.) 
When changing plastic wheels to metal wheels on this car, I moved the washer from the car bolster pivot to the truck bolster so that car wobble is reduced:
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