Once you have a complete sense of the red bucket (deal-changing) items, you will need to negotiate new terms with the seller, revising the preliminary deal you agreed upon. Again, I recommend negotiating these items all together—not in series.
When it comes to the red bucket items, there are a number of ways to protect yourself as the buyer, some more impactful than others. These include:
Ask the seller to fix the problem and continue in good faith.
Insist upon indemnification so the seller is legally bound to ...