What is the proper Tikkun for one who missed putting on Rabeinu Tam Tefillin?
The Rebbe writes1 to an individual that forgot to put on Rabeinu Tam that he should learn the laws of Tefillin and be expert in their laws (it is unnecessary to learn the laws that are relevant for a Sofer like large parts of chapter 32 for example) and 2 or 3 Maamarim that discuss the mitzvah of Tefillin.
Also one should particular to immediately put on Rabeinu Tam after Rashi Tefillin as is brought down in Sefer HaMinhagim page 18. Note, that the Bracha on Rashi covers the Rabeinu Tam Tefillin. Therefore there should not be an interruption in between them.