I have a couple of questions about independent Jackson and Fender Jackson

1) When did Fender take over?

2)Is the quality of the guitars different or noticeable?

1) end of 2002 Fender bough Jackson/Charvel

2) Many people say thats its gone down, not sure how true this is
1. 2002

2. Tough to say. USA Jacksons are almost EXACTLY the same, because the same people run/make the guitars. Some say Japanese Jacksons (Pro and MG Series) have gotten better. I have 2 Japanese Jacksons and love them but I can't say if you will or not. One thing I will say though, is that the Jackson trems are not spectacular. They arent bad really, just not as good as they could be. The low end Jacksons are horrid and you should stay away from them. All in all, pre-fender will gain you envy, and post-fender depends on the series. Just play them and see what you like.
The DK2's are now shipping with real Duncans instead of Duncan Designed pickups and I think the trems were upgraded too. I have a DK2 Pre-Fender and a DK2 Limited Edition from after Fender bought them. The necks are quite different in shape, but I don't know if it's because the production runs are different from the LE runs.