Timing chain alignment, how to manually set timing without damaging the CAM valves?

Hello, I replaced the timing chain components, following the stage 1 and stage 2 set up along with the cam alignment tools. During the installation I couldn't get to line up one of the makings from the crankshaft sprocket, I was one tooth off, I rotated the engine manually to make sure nothing was hitting anything. I put the engine back together, the engine started, check engine light when away, but came back 30 minutes later with bank 1 and 2 system performance and correlation trouble codes. The original chains were stretch due to the high mileage. My question is, how do I manually set timing without damaging the cam valves, I think that I replace the timing chains when the engine was out of timing. Please help, I'm running out of options. Thank you