Why have Chabad taken Rav Sar Shalom Ben Boaz (Gaon) Shimusha Rabbas advice on batim size, 4x4 (2 fingers), also Chabad , and everyone else, has taken Shimusha Rabbas advice with the 4 and 3 sided shin, yet completely ignored his advice about placing from right to left in the batim?

Shalom, Thank you for your question. As to why Chabad chassidim have large tefillin boxes – while I am no expert on Chabad customs, and I advise you to ask a Chabad Rabbi – they have a tradition that the boxes be 2 fingers by 2 fingers. This measure is mentioned in Shimusha Rabba, and quoted in the Tanya, and the Shulchan Aruch HaRav, and mentioned as Chabad custom in the letters of the last Rebbe of Chabad, zt”l. Why these Rabbis chose this opinion is not known to me. As to your question as to why our Tefillin follow the opinion of the Shimusha Rabba about how to put the Shin on the Tefillin of the head, but not his advise as to the order of the parshiot – I see no question. When it comes to ruling halacha we do not necessarily follow one Rabbi, but rather seek to understand the correct ruling for each case. Only when the issues are connected is there a question of if it is possible, or correct, to follow only one of the two rulings. For example, the Shulchan Aruch rules like the Rambam in many places, and in others he rules like the Rashba. But, as long as there is no internal contradiction between the two rulings, this is no problem. As far as I know the issue of the shape of the Shin on the tefillin is not connected at all to the question of the order of the parshiot. I hope this is of some help, Blessings.