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Yep, big-big or small-small are bad combos. They exist, but aren't very useable. Frequently you'll get front derailleur rub in those gear combos, too. Either ring to the middle of the cassette and slightly beyond should be fine.
 
I was running a higher than acceptable cross-chain on my 1x10 (40t) as well. My first fix was to remove my BB spacer to the non-drive side which helped, but not enough so I put a 2mm axle spacer on each of the 4 chain ring bolts to move the 32t inboard (axle spacers fit perfectly over the nut side of chain ring bolts). I now have a nearly perfect mid-cog chainline and minimized the excessive cross-chain in the 40t. Doing so also alleviated my higher resistance during rotation that the OP describes. It also smoothed out the shifting wonderfully, where before it was just acceptable (as in, it wasn't buttery smooth, but felt clunky and mechanical as compared the other nine cogs).

Bike: 2009 Turner 5-Spot

1x10 inventory- Saint M820 RD (stock), Saint M820 shifter, RF NW32t chain ring, eThirteen 40t cog, XT 11-34 cassette.
 
Try something to help isolate your "issue".


Remove all modifications you made to allow the use of a 40t cog, and run 1x10 w/ a standard 11-36 cassette (use new chain and cassette). If you still have the same "issue" w/ the 36t as you did with the 40t, then you know its a chainline "issue".

Or better yet, remove the derailleur from the equation!!! This would only work with sliding dropouts, but loop a chain around the chain ring and 40t cog, then resize the chain, and proceed down the cassette to the 11t.

I am going to pretty much assume the noise and resistance is coming from your derailleur, and not friction from cross chaining.
 
Discussion starter · #27 ·
Did you check that the chain is long enough? That would be my first guess as the cause for resistance.
Good point. Although the chain is long enough to move onto the biggest cog without hesitation, I'll add a link to see if that helps.
 
I know I'm going to sound like a retro-grouch but here goes; I sometimes ride a bike that is old and is a 3x7, if I leave it in the middle ring and just shift the rear it never makes noise. My geared bike came as a 3x8, I spent most of the time in the middle ring and just shifted the rear, no noise. The 3x8 eventually became a 2Ă—8 then a 1x8, no noise from the rear. I broke my shifter and decided to go 1Ă—9, suddenly there is chain noise at ends of the cassette. I can make it go away if the chain is very clean but as soon as it gets dusty, one ride, it starts with the chain noise again. Could the narrower chains be the cause?
 
I noticed years ago that nine-speed was when it started getting tricky to avoid the chain rubbing the front dérailleur. With seven or eight you always seemed to be able to set the gears up very easily. from nine on it gets harder.
 
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