Skinny, please

I used to be byebyeflab (but the URL got taken) and I stopped caring about my weight. I was eating healthy and fell off the bandwagon. After seeing pictures of myself this summer I was absolutely disgusted with how I looked so now I'm trying this all over again. With every goal weight I meet I shall reward myself- because I love buying myself stuff.
Age: 19
Height: 5'5.5"
HW: 177/8/9ish?
LW: 155
CW: 160
Goal 1: 160
Goal 2: 155
Goal 3: 150
Goal 4: 145
Goal 5: 140
Goal 6: 135
UGW: 130

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Bum Knee chronicles

It’s not exactly a chronicle.  But here’s a very frustrating thing in my life.  Last fall I was playing in a Rugby match (yes, I do play rugby) and I felt something “pop” in my knee.  Essentially, there were slight tears on my ACL and Meniscus- nothing major.  However, I was advised to sit out for two weeks and not run.  So I did and I finished the season with a little bit of knee play.  I took our off season (aka, this semester) off and did some working out in the gym.  The plus side off all of my knee problems is that I can easily bike about 15 miles in less than 30 minutes on a stationary bike. 

The bad side: I can’t run on a treadmill and running hills still makes my knees feel weird.  All I want is to be able to run a 5k in August.  I don’t know what to do to make myself be able to run a 5k.  I’ve only done it on the treadmill once and it took be about 40-50 minutes.  

Long story short: does anyone know any good exercises that won’t hurt my knees to prep me for a 5k?