the horse left the barn ...
A leaky roof is anathema to a work shop. Fix the roof by sealing the seams OR cover it with a strong tarp and tie it down. Unless you fix the roof, there's no point in any other preventative methods.
You could build a waterproof box within the garage to store your good tools, but you are fighting a losing battle without a proper building. Spray on 2 part foam is a good insulator and sealant, BUT it's expensive. Good luck on this.
The answer to your question will only be as detailed and specific as the question is detailed and specific. Good questions also include a sketch or a photo that illustrates your issue. (:< D)