No, this is not the infamous what parts do I need

Anyways. I performed the head swap, about two weeks ago. When driving the car, specifically at lower RPMs (1000 - 2500~) I get a really fair share of engine knock. I am taken the timing chain off quite a few times, and have double, triple and quadruple checked it to make sure both cams and crank are at TDC. They are. I just did it once again last night, but when I went to start the car I still got 30ish knocks from start up through about 30 seconds or so.

Knocks are being registered through K Pro, I am using a fellow EPers tune from when they had their car dyno'd with an A2 head. The setups aren't exact, but very similar. I know that some adjusting will need to be done, but should I really have this many knocks? I really don't want to drive the car around when its knocking that bad just at idle. Any other ideas on what it could be besides the timing chain being off?