Thats what sucks about OEM Toyota ECUs. they are locked down tight. I think that after all those changes to the engine that the computer is probably having difficulty trying to get the OEM parameters back in check. I would try to single out the obvious first like timing, Fuel, Check for vacuum leaks etc. Then install a simple wideband and see what it says. Get the engine broke in, re-check valve lash, considering that the head was probably decked that would mean it sits closer to the block therefore cam geometry/timing has changed slightly. anyways those are the obvious details. hope some of it helps. Good luck. it looks like a decent build. those engines are tough. it might out live you now haha.