As the title says, I put in heavier springs on my bike, slapped everything back together, and now my right clip-on is turned in more compared to the left when the front wheel is straight. The clip-ons are on the same, both as far out til it hits the stops. Why is this, and how do I realign it?

 

Just loosen the two bolts holding the clip on to the fork, turn it to the desired angle then tighten the bolts.

 

Yeah I know I can move it a little, but the clip-on stop rests between the top triple pinch bolts. I had the clip-ons all the way out, as far as they go, before I changed the springs and everthing lined up fine.
Now, after everything is back on, with the front wheel straight, the clip-ons feel slightly turned to the right. So basicaly when I feel like I'm steering straight, the front wheel is a little off to the left.
I guess I'm wondering why it was lined up before and now it's not.

 

IIRC, you're supposed to install one fork and barely tighten the bottom triple. Then install both forks and the axle and torque the steering stem bolt. Then align the forks at proper height and tighten the top triple's bolt then bottom, then clip ons.

That's off the top of my head, but the procedure is in the manual. It's meant to help you get it true. If it still doesn't work, check your torque specs and then ensure you have a straight axle and forks. If it doesn't help then you've got a tweaked lower triple.