Yes, you must file form 5329 but I would send a copy of the letter and keep the original. I have another post with step by step entry all the screen shots to ask for waiver.
If you want to send the custodians letter, you will need to print and mail your return. I have another post on mailing a return.
Reference: About Form 5329, Additional Taxes on Qualified Plans (including IRAs) and Other Tax-Favored Accounts
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