I believe there is no way to confirm whether they got your GRE and TOEFL scores. If the LORs and transcripts were sent via registered mail, you get a notice saying who signed for your packet, so this serves as kind of a confirmation.
Poke around on their webpages for long enough. I know MIT has a checklist for each candidate, but I'm not sure about the others. Some schools also send emails when your application is complete. Also know that there's sometimes a delay between when the university receives your paperwork and when the department gets them, so if it takes longer to show that the department has your stuff that's why.
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