Every time you change your suspension in some way you effect the geometry of a well designed and balanced "system" A change here necessitates a change elsewhere.
You have to lower the back when you lower the front.
Think of a shopping cart wheel, with out the proper angle it will wobble and the faster you push the worse it gets.
Make small changes and take it slow, short rides around the block before you hit the highway.
I have my front end lowered about 2 1/4" and the back about 2". I just got the front 3/4" lower last night by butchering, I mean notching my handle bars.
I have just discovered the better way to lower the front by shortening the fork tubes with internal spacers.
Lowering the fork ride height.
If you lower the bike you will need to modify the side stand.
There are a couple of scary suspension failure stories there that are worth the read.