The proper way to file Form 5329 is attached to Form 1040-X.
Form 5329 can be mailed by itself only when you are otherwise not required to file a tax return.
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If I read your post correctly, here is described in great detail for another taxpayer the same situation
albeit with some extraneous issues you can ignore.
https://ttlc.intuit.com/community/after-you-file/discussion/excess-contribution-to-ira/00/3082275
Replace text "traditional IRA" with "Roth IRA" and 5329 Part III with 5329 Part IV
@kaitech3
