I don't switch my client's EIN's simply when going from LLC to S-Corp (you just use Form 2553). There has to be more to it. Sending a notice of your S-Corp acceptance under your old EIN to the state agencies will get them to process the change as a name change and not a discontinuance, generally speaking.
Lets start with Section 351 itself:
§ 351. Transfer to corporation controlled by transferor
(a) General rule No gain or loss shall be recognized if property is transferred to a corporation by one or more persons solely in exchange for stock in such corporation and immediately after the exchange such person or persons are in control (as defined in section 368(c)) of the corporation.
§ 357. Assumption of liability
(c) Liabilities in excess of basis
(1) In general In the case of an exchange-
(A) to which section 351 applies, or
if the sum of the amount of the liabilities assumed exceeds the total of the adjusted basis of the property transferred pursuant to such exchange, then such excess shall be considered as a gain from the sale or exchange of a capital asset or of property which is not a capital asset, as the case may be.
In other words, no, you cannot set up a goodwill account for tax avoidance purposes. Sorry there.
Good luck and let me know if you need more clarification.
Thank you for your question.