Why did he say "Ki Yada
Malbim: My knowledge of and recognition of my sin is sufficient punishment.
Why did he say that he came first?
Rashi (from Shochar Tov 3): All of Yisrael sinned against you, and I, more than all of them. If you pardon me, all Yisrael are confident that you will pardon them. If not, they will fear to return to you (Radak - to make Shalom with you).
Why does it say "Beis Yosef"? Shim'i was from Binyamin!
Radak: Binyamin, Efrayim and Menasheh are all called Beis Yosef, for Yosef was the head. 1
Radak citing Shochar Tov 3, #1: He told David, Yosef's brothers did bad to him, and he was good to them. So I did bad to you - do good to me!
Radak citing Shochar Tov 3: All of Yisrael are called Yosef - "She'eris Yosef" (Amos 5:15), "Noheg ka'Tzon Yosef" (Tehilim 80:2).
Efrayim led the Degel consisting of these three tribes (Bamidbar 2:18-24). Binyamin called Yosef his 'Rosh' (refer to Bereishis 43:30:1:1*). (PF)