<<Will lowering links kick the front end out and make it handle worse? >>
This will take away it's cornering ability, you put more weight bias on the rear of the bike, vs the front. I have a KLX and found the best way to make my KLX turn better, is to pull the forks up through the triple clamps 5 to 7 mm. The only problem with doing this, is throwing off the balance of the bike, but I'd trade off some balance for some more turning ability (Preference).
You may want to consider doing both (pulling forks up through the triples and putting on lowering links (dog bones), to lower the bike. I'd still be inclined to pull the forks up through the triples even more.
BTW - You could put more preload on the rear spring to put more weight on the front end, but then you get into rear sag, it also raises the rear of the bike etc. and that's a whole new set of issues to resolve.
Hope this helps !!! -MC-