I've been working on my 4runner for a few months now on and off getting down to the heads to replace the head gaskets. i successfully replaced it and have begun to reattach everything i took off. while putting the timing chain back on i lined up both cam chains correctly and had the timing chain positioned right on the crankshaft, the book told me to rotate the crankshaft to give the whole thing two rotations to ensure the pistons were fine before i moved on. fortunately i encountered no problems with the pistons but i noticed when i got back to top dead center the colored links in the chain were off. the timing marks were fine but the marked links were all moved forward by three. i also saw that the cam links were off as well, although like the timing chain the timing notches seemed to line up fine. my question is whether or not the colored notches mean anything or if they're just there to help with the positioning of the chain. id really appreciate the feedback i don't want to go any further without assurance that the timing is fine, thanks guys

Disclaimer: I don't have a V6, nor have I done a timing chain job on one of these.

If all the timing marks line up after rotation, you're fine. Unless the number of chain links is some integer multiple of crank / cam sprocket teeth, the chain will only occasionally be in phase with the crank / cams. Sounds like each rotation it walks forward 3 teeth.