(disclaimer, I have no book learning about what I am talking about)

I realy don't think the chain position has much to do with it. On TDC on compression as long as the crank and cam are properly position, what color does one link have to do with it? It should take 2 turns of the crank to get the cam at the same spot on a 22RE/R/RET/REC. AT TDC the gas is compressed, then the spark ignites and the crank turns. On the up the exhaust opens and lets out the bad gas. Then at TDC on exhaust stroke the exhaust is starting to close, and the intake opens and sucks more gas in on the down stroke. Once it goes back up it is compressed and it starts all over again.

Chain length is sized so that it can go around both sprockets and the tensioner. has nothing to do with the timing other than it pulls. Like the chain on a bike, if it is one link longer, you just move the wheel back. still pedels the same.

(majority of this post is for a newbie who may be reading and learning something new. As I started rambleing I forgot what the question was!)