The stock aircraft shouldn't enter into the problem. The MiG-29, F-16 and F-18 should be the only planes you have to change values of. I haven't found any of that data in the stock aircraft data files either. If you modify the start and end service dates, you should be able to fight the -29 with the -18 or -16. WoV will have you face off against any aircraft within the listed years years; so it is surprising that you aren't seeing the -29 in your engagements. Of course, you could always modify the start year to say, 1970 for all three planes, which could make the -29 more likely to show its face, but at the same time, you'll have to switch it back unless you want an ungodly challange when you fly the F-4.
I guess there's some randomness to it also; when I was flying my Tomcat, I splashed 8 MiG-23's, and searched for new targets. I ended up finding a small flight of Japanese A6M2 Zero's (other add on a/c that I got). Also, when I fly the F-15, F-16 or F-18, I normally encounter MiG-29's, MiG-23's or MiG-21's, randomly Mirages. Maybe it's just bad luck? Anyways, if all else fails, you could make the start dates around 1990 or 2000 for all planes, then you'd probably only run into -29's...or I'd think at least.
Good luck