With that chain (it is stretched a little bit), that's the best your going to get, (your lined up).
***With all the mods, timing, etc, you plan on doing / have done, I'd replace that chain. Check the sprockets and very likely replace the rear chain tensioner guide, (rear) that gets a bunch of pressure with the chain and CCT working against each other.
There is NOTHING ELSE between the crank and exhaust cam to have that NOT line up, period.
If you wanted to see (just for S&G's), you could move either cam a tooth and see REALLY HOW FAR OFF THEY ARE THEN...
How many miles on the engine?