You did everything correctly- you mailed the 709 by certified mail so there will be a record of it so the 8892 is probably not necessary. The IRS is processing a lot of returns now so it is taking longer than normal. The IRS is also good at working with people so even if something happens, the certified mail will be enough to show you made a good faith effort.
The problem with sending the 8892 AFTER you already mailed the 709 is that if they get processed in order, it may confuse the system, but if you want to send it, regular mail to the Kansas City campus is correct.
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