have u got a pic of the bike i can tell just by looking at it if the front forks have been lowered or messed with, as for the back suspension just look at the diagram don put up and you'll see how that should be, lowering makes a bike look nice and aggressive but they don't ride worth a crap when they are lowered, it messes up the geometry of the bike and you can't lean as far, and they don't handle as good, it's not like lowerng a car, i've got the ajustable links that will lower it 1 1/2 or 3 inches, or just leave it stock and i only lowered it 1 1/2 and didn't like it and raised it back up, so i know where you are coming from.

 

Here's a photo of the bike. http://home.comcast.net/~jdthorstad/newbike.jpg

 

t-bone it looks like your front end hasn't been touched, you will need to replace those parts that you have and what it will do is raise your tail back up just look right in front of the back tire and you will see the shock at the bottom end of the shock is the lowering link it's the two flat plates, it will be connected to the dog bone that is connected to the frame you will need to find a way to get the pressure and weight off the back of the bike, i use a engine hoist, you could use whatever you think will raise the bike and keep it stable remove the bolt that runs through the bottom of the shock than remove the bolt that connects to the swing arm and then remove the bolt holding the dog bone to the frame now you just put the parts that where in your pic back on just like you took them off, you probably have to raise the bike a little to get the lowering link bolt in cause the swing arm will know need to be 2 inches farther down so the tail will raise up 2 inches, if you need more help or a little advice on setting up your suspension just let me know or anyone on here should be able to help, hope you get it fixed.

 

that bike looks clean