Are you taking the time to do dynamic stretching before you run?
Have you upped your carbs to provide for all of the added running mileage?
Remember that what worked for you while riding doesn't translate into running. You burn twice the energy in half the distance while running. You need to fuel and adjust training technique. Also, throw in an extra rest day when needed, that isn't a problem unless it is every other day.
When I start upping my mileage, my wife starts making large lasagnas twice a week. When you are going to have a long run on a hot day throw in a banana split for a treat and the readily available sugar. My wife thought I was crazy but I had such a good run later.
You should also look at electrolyte/carb drinks for while you are running. You are going to need to learn all of these tricks and more between now and your 100 mile run.
Do know what Ultra Runners call a marathon? A warm up.