Leaving the forks alone, will leave the ST handling like a chopper. With an aftermarket "standard height" rear shock you can raise the fork tubes to 5/8" successfully. Anything after that you'll get head shake at around 40-45mph with certain brand tires. However, you are getting a custom lowered rear shock. Try raising tubes 5/8" and go from there. I woudn't raise any more than 3/4". Getting a new rear shock will certainly change the handling for the better. But, because your dropping the back and raising the front forks to try and equilize the bike, I would for sure freshen up the front end to combat the front from bottoming. Your gonna need fork springs and a fork oil change matched to your weight. Another thing to consider, is your gonna lose ground clearance. If your any sort of an aggressive rider, the pegs are gonna touch down early.
After the fork tubes are raised, you should remove the front wheel and check front wheel axle alignment between the tubes. Axle shaft needs to slide as smooth as butter between the tubes, before torqing everything down and re-installing the front wheel.
Starting off with a custom lowered seat should have been your first move, before messing with the suspension.