Background:06 WRX TR-90k mies-Cali 91 Octane

Story: Due to transmission issues from the previous owners modifications, I had to replace my transmission about two weeks ago. Now I am having two issues. The first is that the cruise control does not work. I can click the button which turns the cruise light on, but I cannot set a speed. My second problem is the car seems to stall when I am at low rpms (under 2k) in second gear. When I depress the clutch pedal, the engine will stall. This has almost caused some accidents due to loss of power steering. A new clutch was also installed when the transmission was swapped.

Side note: This was after the issue was occurring: I just installed an COBB intake and when I was installing it, I found out that the hose clamp connecting the post MAF tube to the Airbox was completely lose the tube was just on the airbox. The stalling continued to happen after tightening the clamp. Also before I got the transmission swapped, I had gotten two CEL's that have both came up twice, I cannot remember the exact codes but one was "Engine lean bank one" and the other one was a secondary valve was stuck.