First, what do you mean by "...not damage the factory paint job."? I'm assuming that if you apply any extra paint or weathering to your model, you're "damaging" the factory paint, since it become immediately evident the factory paint job has been modified.
The photos of weathered models look really good, but they might be dirtier than you want. Although brushing the louvers improves their looks, when you observe the photographs of dirty louvers, you'll see that their darkness is pretty well confined to their rectangular outline, and not just a blob of darkness in the middle of the group of louvers.
Here's what I do to emphasize louvers.
First, I disassemble the body on my Geeps, removing the walkways, handrails and cab.
Then, I de-grease the body using Bestine rubber cement remover, which is available at most art stores. If you can't find it, a wash of mildly soapy warm water will do the trick, but you have to let it dry overnight, or air-dry it with compressed air.
Next, I mask off the louvers and vents so they are exposed and everything I don't want to blacken is masked. This gives you nice, straight, square edges and sharply defines the areas you are going to blacken...just like the photo you provided.
I use my airbrush to dust on a layer of flat black acrylic paint such as Floquil Polly Scale grimy black, or engine black.
Then, I use a paper towel dampened (not soaked) with alcohol to lightly wipe the black dusting off the tops of the louvers. You can also airbrush your vents too and wipe them, but I usually brush paint them. You need to do this after the paint has dried, but has not yet cured...like five minutes after you've sprayed it.
Next, if my reference photos say I should do this, I'll spray a really light coat that allows the stock body color to show through on the louvers. If you get it too thick, just do the wiping trick again.
Next, you can usually brush paint the vents and fans since they have structures around them to guide your brush. I also do the wiping trick with them after the paint has dried
Next, I take off the masking tape, reassemble the body and weather it up with washes, more airbrushing or powdered pastels...to whatever dirtiness I think looks appropriate.
If I've got the louvers, vents, and fans too dark and they've cured, I use a new pink rubber eraser to lightly rub those places and remove paint until I'm happy with the results.
In my opinion, the sharp lines that masking gives the darkening of the louvers, vents and fans gives the bodies a more prototypical look than just hitting the middle of these items with a blob of weathering, although the blob weathering looks better than no weathering.
This masking and wiping technique works really well for light-bodied Kato F-3's.
Here's a shot of some detailed up Katos I painted several years ago using these techniques, but layering the darkness in three consecutive un-maskings.
If you don't have an airbrush, you can do this using flat black model paint in spray cans, and using paint thinner instead of alcohol to dampen your paper towel. It requires a very light touch however.
Good luck! Weathering for the first time is always an intimidating jump into the dark, but very rewarding especially if you start weathering using specific prototype photos as guides for your efforts.
Cheers!
Bob Gilmore