You don't answer a CP-2000 with a 1040-X, so the 1040-X instructions are irrelevant.  Follow the CP-2000 instructions, which tell you not to file an amended return.    You check the box for total or partial disagreement, and explain your reasons.  If you want to contest the Section 6751 penalty, you can do that, but it's difficult when you fail the $5,000 test.  

The next step should be for IRS to send you a revised CP-2000, including a revised penalty.  But it's getting close to the end of the fiscal year (September 30), so don't be surprised if they just rush it straight to Notice of Deficiency.