1)
Why did Efrayim complain? What did Yiftach do to them?
1.
Malbim: They were upset that Gil'ad chose Yiftach to lead all of Yosef because he won the war. They asked why he did not call them to fight, and wanted to burn his horse. Efrayim is greater than Menasheh - "va'Yasem Es Efrayim Lifnei Menasheh" (Bereishis 28:20).
2)
What is the meaning of "va'Ya'avor Tzafonah"?
1.
Rashi: They crossed the Yarden and went north, to where Yiftach was in Gil'ad.