I was able to find some formulas on the Cardinal scale manufacturing Co. web site for placement but I am still having trouble finding information about Gondola sizes'.

Don't worry about the gondola sizes per se.
Either:
a. BNSF contract specs should indicate the placement and clearances they want. Or is this on private track?  

or:

b. Get the AAR clearance charts.
 B plate or C plate cover cross section of car shapes. B plate is slightly smaller, covers about any place on North Amer railroads.  C plate a few inches bigger, covers about 98% of North American locations.

  Actually, you want the diagrams for structures and buildings which are larger than B or C plate for the cars. I only deal with equipment, so don't know what the building diagrams are called.

  Cross sections ONLY apply at tangent level track, straight line. There are swing in and swing out calculations that have to be done for horizontal and vertical curves.  AAR uses a 'standard base car' of axle and truck centers and overhang. The clearances are based off that car. Longer cars, or cars with longer end overhangs, have to be narrowed at certain points so as not to exceed swing in or out in curves. There are also calculations for dynamic conditions, bounce, rock side to side, wheel wear, spring sag, etc.
    Everything we do is packed to the limit for space, so all these calcs are necessary.
     You may be on straight level track, no dynamics, and life may be simpler. But I would start with the AAR plates.