1. I think that the ALS for the 13L has been set up wrong - concerning the charts it has to be an ALSF-II-type ALS (have a look at Google Earth e.g. - they are made correct with 04R - a special thanks for that) but the type installed is unknown to me. And very strange are the yellow flashing lights. Are this the real ones?
Not exactly. 13L has an ALSF-II AND RLLS with 6 sequenced flashers, it's not a standard ALSF-II like 04R. The scenery has the flashers correct, I believe we missed the ALSF-II part, but it's already being fixed in the update.
2. The same is for 13R: Yellow flashing lights? If I remember correct from my last visit some (many ;-) years ago there can (!) be ODALS?
13L has ONLY RLLS with 7 lights, just like the scenery. Perhaps the yellow color is not exactly spot-on (it's more like reddish/white color), but it's surely not pure white like ODALS would be.
3. Is there a chance to get 3D-ALS for 13L and 13R?
4. Is there a chance to get 3D-VASI- and 3D-PAPI-boxes all over the airport which are missing for now?
We'll see, JFK is not a place where we can waste many polygons, 3D support for lights are fairly complex. Not for us to add, but for FSX to render.