Probably homemade parts, maybe Shapeways

Assuming that you're talking HO or O scale, I'm not aware of any suitable parts currently available specifically for the RS-11 louvers, but there are a couple of options. In N scale, it's actually easier.

Precision Scale has offered a set of HO scale ouver inserts for RS-3s that it might be possible to cut in half and use for the smaller louvered boxes (see  http://www.walthers.com/exec/productinfo/585-3908, regrettably not in stock as I write this). This wouldn't get you out of the woods for the larger aftercooler(?) box, however.

At one time, I would have suggested Tiger Valley Models as a possible source for HO scale parts, but I cannot find confirmation that it is still in business, or find a product listing. (Can anyone tell me whether it's still in business?)

There is a set of 3D-printed louvers for this exact conversion, but only listed in N scale, on Shapeways right now (see http://www.shapeways.com/search?q=RS11+Louvered+Filter+Set). You might be able to persuade the person who set those up to scale them up to HO. If you're doing this in N scale, this would be your solution, right here.

The other alternative would be to cut the boxes from pieces of .030"-.040" thick styrene, then apply Archer resin louver decals to get exactly the appearance you want. The Archer set that would be a start for this would probably be their HO scale 14" louver set (AR88038) , as seen on page "4" of their catalog, or their HO scale Resin Railroad Louver Mix set (AR88056) on page "6" of their catalog at  http://www.archertransfers.com/ASSETS/ARCHER%20SD%20Catalog.pdf. They have N and O scale versions of these sets as well.

With the 14" louvers, you might need to cut the louvers to the correct width, but the Resin Railroad Louver Mix set offers louvers in 14", 12" 9" and 6" widths.

If the person who drew up the N scale louver set would be willing to scale it up to HO scale, that would be the easiest route (assuming were talking HO scale here). Otherwise, I think that the styrene and Archer louver decal route is the most certain to provide satisfying results, especially since it offers a path to making the larger filter box you'll need on each side.