Hold off on any supplements for now. At best most are probably unnecessary. At worst they can do harm (even legitimate ones).
A good example? I know a lot of people who take MSM, Glucosamine, and/or chondroitin to give them "healthier joints". While these supplements do wonders for osteoarthritis, they can actually be detrimental to your connective tissue by disrupting healthy collagen formation. I know at least one person who developed tendinosis while on these supplements and his proteoglycans and glycosaminoglycans were through the roof.
First off, what do you mean that running "shocked you"? Were you experiencing pain or discomfort? Please be specific.
In general a runner's diet should just be one that is generally healthy. Unless you're doing serious distance running you don't need to worry about things like carb loading, and even if you are it's too soon for you to be concerned. Before you can carb load your slow twitch muscles need to adapt to increase their mitochondria count and their glycogen storage capability, along with your liver's storage.
For connective tissue specifically, the only thing you need to be particularly careful of is your lysine intake. Lysine is an essential amino acid that's very important for collagen production. Of the three primary amino acids in your collagen it is the only essential amino acid. The other two the body can synthesize in a pinch.
Recommended dose of lysine is 12 mg per kg of body weight per day. It's commonly found in milk, eggs, chicken, beef, certain fish, and quite a few pulses as well. Usually 5-8% of the protein content in these foods is lysine.
Simplifying the math for you, you want to take your body weight in kilograms and multiply it by 0.24. That's how many grams of protein you want, each day, from these foods. Full list can be found here: http://en.wikipedia.org/wiki/Lysine#Dietary_sources