Three month running hiatus and now what?

I have struggled with right sided knee pain for a few months. Before that I was running 5K 3-4 times per week.  I wasn't running with any goal in mind, just for fun and fitness.  We live in a VERY hilly area and the hills are more like small mountains, which has always made running a challenge for me.  I became very used to the hills and so that made my running on flat ground a breeze, but with that came some knee strain and then it was all aggravated by an actual fall onto the knee which was not related to running at all. I was planning on running in the Cape Cod half marathon which took place a couple of weeks ago, but could not train for it.
For me, the biggest fear of not running is losing all the fitness I have gained over the last year. Remembering that I couldn't run to the mailbox initially and worked myself up to running four small distance races per week! So now the procrastination builds as I worry about how difficult that first run is going to be again. This only causes more time to go by and before you know it, it's three months and I've lost a good amount of muscle. During this time I also lost weight.  Some of it I'm sure is from the muscle loss but my diet has remained very healthy and wholesome and has not allowed me to put any weight back on.  Nutrition is always the most important thing in my mind, exercise is only secondary.  I've been able to maintain a certain level of fitness and health just through diet alone and this hiatus has helped me prove that.
So today I put on my running sneakers and heart monitor and headed out the door.  I warmed up longer than usual ( about 20 min) and then hit the road. I ran my usual run and all it's hills.  Here are the differences I noticed:

Three months ago:

5K on hilly terrain average time 22 minutes
Heart rate on flat areas 110 bpm
Heart rate on hills 145 bpm
(My aerobic threshold is 160 bpm)
No walking or resting
No pain, shin splints or side stitches

Today:

5K on hilly terrain average time 33 minutes
Heart rate on flat areas 130 bpm
Heart rate on hills 160 bpm at aerobic threshold
No resting, walked briefly up part of a large hill
No pain, no shin splints, no side stitch

A certain amount of fitness has been lost but I feel confident that I can slowly build back up to where I was.  That is not even really a goal for me, the true goal is to physically leave the house and move my body! I feel great post run and I am over the anxiety of how that first time back out is going to be. I will of course listen to my body and take it easy. Hopefully I'll be running a half in the spring and if not, I will still have the benefits of regular exercise.