Here's a screenshot of the recently deleted NewTIS premium timing chain replacement procedure, showing measurements of the locking tool gaps.
However, you shouldn't be worried about the first couple minutes of cold engine performance. The ECU isn't happy until coolant has reached a minimum temperature. Can't remember the details, but right after my first tune, one of the temp overrides was overlooked and I threw a code if I got on it before this minimum temperature.
Personal opinion --- cold engines shouldn't be driven hard, or stressed enough to notice "bad" performance. If it cold-starts normally and drives OK after heating up, live with it.
If it's not engine timing or compression you'll need to start looking at fuel and spark. Some decent diagnostics kit with live data should help narrow it down.
I would start looking at obvious things like alternator output and fuel rail pressure first then look for any reasons why the ECU might be cutting fuel due to detecting an issue. I would then look at fuel correction on all cylinders to see if there's one looking very different. Start with that and see what you find...
So i have seen a few things cause bad colds starts. the most obvious is the high pressure pump may be faulty. can your scanner monitor rail pressure?. do the plugs look fouled at all? One other item that is constantly over looked is a faulty coolant temp sensor misreading which cause hard starts. the waste gate thing is odd though. Out lier could be a faulty head gasket sealing. when you turn off the hot engine, a little bit of coolant squirts into the cylinder as it cools causing a misfire at cold start until it clears out.
pretty awesome build though!