1)
Why does the Torah place Menasheh before Efrayim here, when in Bamidbar, 1:22 & 24, it gave precedence to Efrayim?
1.
Oznayim la'Torah: In Bamidbar, where Efrayim was more numerouus than Menasheh, the Torah gave precedence to Efrayim, according to the ruling of Ya'akov. Whereas here, where, beised being the firstborn, was also the larger tribe, the Torah lists Efrayim first, as per the request of Yosef. 1
1
See Vay'chi, Bereishis, 48:19 & 20.