As the welder, you are between a rock and a hard spot. As they say, "S___t rolls downhill" and your on the downhill side of the problem.
You are an employee of the company. The employer has the responsibility to provide proper direction to you, the employee. There is little you can do if the company doesn't provide the proper direction and the proper equipment and materials to do the work correctly.
You have attempted to tell them the welding rod isn't stored properly. Did you tell them it had to be stored in an electrode oven (not a kitchen range) at 250 degrees F (or higher)? Did they ignor your warning? There's little else you can do. I've been there before and I had to made a decission to continue being the "whipping boy" or find a new employer.
One other thing you can do is contact the manufacturer and ask them what the recommended procedures are for the repair of their equipment. They may be willing to recommend the proper preheat, proper filler metal, and techniques to be followed.
You may have to make a decission and look for a different employer, because those types of companies aren't usually interested in doing it right. They just want someone to blame when it blows up in their face.
Good luck - Al