Bicycle Mechanics - chain noisy, chainline?

I just rebuilt my roadbike with all ultegra parts, the front derailleur, chain, bottom bracket,and shifters are new and the double crankset, rear derailleur, and cogset are very lightly used. Anyways when I'm on my top three largest cogs and on my 39T chainring, my chain seems noisy, near the chainrings. The chain is not touching my front derailleur but the chainline also isn't completely straight which I think where the problem may be, because when I move further down the cogset and the chainline straightens out it sounds nice and smooth. I never had this problem before, am using the same hubs and all as before. Suggestions on what I can do to fix this problem? If my description is hard to understand write back so I can clarify.

My bet is that your chain is rubbing the inside of the big chainring. That's common on bikes with short chainstays.

The most common partial solution is to fit a 2mm spacer behind the bottom bracket. I tried that on my Klein and it helped, but it wasn't enough to eliminate the issue.

It was suggested to try a genuine Shimano chain because it's a tiny bit narrower than a SRAM, but it didn't help.

A promising solution that I haven't tried is to fit an XTR bottom bracket with a 116mm spindle. That would space the crankarm out an additional 2mm (over an Ultegra BB with a 2mm spacer) and center the crankarms again. Hopefully it would be enough to completely eliminate the problem.

Right now I've got an FSA compact crank on my bike that rubs in the three smallest cogs (with no spacer). I don't worry about it. I just use the rubbing sound as a reminder that it's time to shift into the big chainring.

I actually meant the larger cogs, like the 25T cog, not the 11T cog.

I just rebuilt my roadbike with all ultegra parts, the front derailleur, chain, bottom bracket,and shifters are new and the double crankset, rear derailleur, and cogset are very lightly used. Anyways when I'm on my top three largest cogs and on my 39T chainring, my chain seems noisy, near the chainrings. The chain is not touching my front derailleur but the chainline also isn't completely straight which I think where the problem may be, because when I move further down the cogset and the chainline straightens out it sounds nice and smooth. I never had this problem before, am using the same hubs and all as before. Suggestions on what I can do to fix this problem? If my description is hard to understand write back so I can clarify.If you used the 109.5mm BB the chainline is as good as it gets.Did you remove the crank self extractors and bolts to be able to the line up the BB splines and crank arm grooves, and then use enough torque to insure the crankarm was fully seated?

I actually meant the larger cogs, like the 25T cog, not the 11T cog.

Oops.