My question is, lowering the front end did I change the geometry enough to cause this problem?
1/2" is a lot of change in the front ride height. My usual advice is change it by less than 5mm at a time. Can you push the forks down a bit to see how it changes things? (even if you need to test ride it with the fork caps recessed a little into the clipons...)
I'd re-check your steering head bearings too it you tweaked them, I'd also look carefully at your rear tire - if it's getting a bit shagged and squared off I'd try replacing that before changing too much else, it might be that the geometry changes have made it a little more sensitive to rear tire wear...
big