The only thing you enter from the 5498 is your contributions to IRAs, which might or might not be deductible or over the limit.
A custodian-to-custodian rollover will not generate a 1099-R (certainly not for an IRA, not certain about a 401k to IRA).
You enter Roth conversions by entering the 1099-R that shows the conversion and answering the interview questions about the conversion. For example the 1099-R for the conversion will show the conversion amount and box 7 code might be 2 ("early dist exception applies").
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