Eventually, on all my cars, I was planning on improving the running boards with either direct replacement with Plano etched SS running boards, or snipping the mounting pegs off of MTL running boards, sanding them thinner, then gluing them on. Other cars from other brands would get similar treatments depending on the models.
However, now that Plano is out of business, that part of my plan probably isn't gonna work any longer, so, looking at newly manufactured models of cars that have running boards, it appears that the newly manufactured ones have vastly improved running boards over most cars from 20 years ago or longer.
But, some are just re-runs of old models that still have grossly oversized running boards, most of which can be either sanded down after snipping off the mounting pegs or replaced with MTL running boards...which used to be readily available and still might be relatively easy to get...most of which I still sand down.
Most of the time, I don't fill the mounting holes in the carbody, as they are underneath the running boards and are mostly not visible. However, in some cases, they
are visible, so they get filled with the mounting pegs I've cut off of the running board, glued in place with my Tenax-7R equivalent plastic welder and snipped close to the car roof, then filed/sanded flush, with a dab of paint that approximates the roof's color.
For my Plano running boards that I have left, I glue them on with canopy cement, applying a dab on two or three running board standoffs on one end of the car, making sure it's aligned as perfect as I can...and I hold it until the canopy cement is capable of holding the running board without my fingers pressing down (maybe 5 minutes). I let it dry for an hour...or, I help it along with my old shop hair dryer set on "Medium" heat (so I don't melt or warp the plastic car body). This speeds things up a lot...then, using a long, thin detail brush, I apply a small dab of canopy cement quickly on the rest of the standoffs, trying to only get it on the standoffs' very tops...then, I press down on the running board as evenly as I can, sometimes using a narrow steel rule until the glue starts to cure, then I help it along with my hair dryer again.
If you get some canopy glue slopped onto where it shouldn't be, you can easily remove the excess using a small fairly stiff watercolor brush that's wet with water before the cement fully dries.
Canopy glue is great stuff and dries very transparent and thin, and holds all sorts of varying materials very securely. I use it a lot.
OR, I use my Tenax-7R plastic welder substitute
methylene chloride (or dichloromethane) (you can buy it at your local chemistry store) which is what Tenax-7R was, to chemically weld the running board standoffs to the bottom of the sanded-down running board, using a small brush. Don't apply too much, and use a slim brush that's smaller in diameter than the gap between the car roof and the bottom of the running board trying to hit the joint between the top of the standoff and the bottom of the running board. This doesn't work for metal running boards, only plastic ones and not Delrin or other acetal plastics.
I don't find it necessary at all to use Epoxy, or sticky glue such as Walther's Goo, both of which are difficult to apply precisely.
Although I haven't done it, another possibility might be to use Artist's Matte Medium, or Mod-Podge Matte, which I think would be similar to Canopy Cement...especially for metal running boards, but might take longer to set up, but wouldn't be glossy.
Close-up photos don't lie, so...
Photo (1) - ...here's a close-up of a UP CA-1 caboose kitbashed from a couple of MTL Wood Caboose with sanded-down running boards viewed from the side, showing a complete lack of mounting pins...glued securely to the car body using Tenax-7R:
Photo (2) - Fine N-Scale resin kit with an etched brass running board attached with canopy cement to each running board standoff: 
Although neither of these examples is of MTL's perforated running board, I am assuming either method I've described above would work to securely attach one to your old Bachmann boxcar...just snip off the old Bachmann mounting pins to fill the holes if you need to do that.
Cheerio!
Bob Gilmore
(edited for typos and grammar)