Looking for 3rz fe timing advice

I have a 04 Tacoma with the 3rz fe 2.7 and I am in the process of replacing the head due to low compression in cylinder 3. Seems to be the result of a “burnt valve”. I lined up the cams and the HB to TDC, I have been watching videos on YouTube and referencing the Haynes repair manual since this is my first time replacing a head. I noticed that the colored links on the timing chain don’t seem to be lined up with the chain sprocket. I took some pictures and would appreciate any advice as to how important the colored links are to the actual timing of the engine.

 

as long as its on TDC and timing marks on cam sprocket/HB are right I wouldnt worry too much about the marks on the timing chain.

 

Im assuming you are checking this with the head on right? Would be hard to tell if everything is lined up as pictured above

 

Yep, I set and checked TDC with the head on. I only noticed the chain marks now that I’m scraping the head and rewatching videos getting ready to put the head back on. I appreciate the advice! I bought the truck 6 months ago and was told it just had routine maintenance done to it nothing major including being the original head and gasket at 240,xxx miles on the truck.