So I recently got a new frameset and after installing my 2013 sram red on the bike I cannot seem to get the rear to shift properly. A little background, I have installed this groupset on two other bikes previously, a giant tcr and another altamira (different size), the cables on this bike are externally routed which makes this a bit easier. I work at a shop and think of myself as fairly experienced when it comes to tuning bikes but I can't seem to figure this one out. So let's go through a few of the issues I have elminated.
chain: used a chain checker, it is good to go
cassette: have tried 5 different cassettes
wheel: I've tried 4 different wheels
hanger: checked this up and down and also front to back, good. I have even tried alignments that are not straight in an effort to line up the derailleur cage more precisely with the cogs
cable routing: I always route the cable around the back of the bar, I have routed two sets of cables, one straight and one crossed under the down tube
cable guide: the original guide that came with the frame was pretty messed up so i actually put one from my old altamira on. I also routed the crossed cables with a plastic protector running the whole length which helps the cable run smooth through the guide.
rear housing loop: I have run both small and large rear loops, my friend is a pro tour mechanic that works with the new sram and said i should go with the big loop which i have done
rear derailleur: I put on a rival rear d and the issue was still there
shifter: although i have not used a different shifter the shifter feels smooth upshifting and downshifting when no connected to the derailleur

The actual shifting issue: when shifting towards the 11 tooth there are hiccups around the 14tooth and 13tooth. Shifting from 13 to 12 and 12 to 11 is good.

My thoughts: There is some way that there is still too much friction in the cable/housing setup causing me to overcompensate with cable tension or something is wrong with the shifter that I cannot detect.

The kicker: I have just installed my friends old ultegra right shifter and rear derailleur. This set up is not bad, it seems to work better than the red but still from the 14 to the 13 it hiccups.

so is it possible that something is wrong with the frame, that somehow the cables can't be routed smooth enough or some sort of alignment issue in the rear end? Please play devils advocate with everything I have done so far, I feel I have been very thorough but I'm sure I missed something.

Try a new rear shift cable?

^this. And Make sure Cassette is tight(seems stupid but happened to me)

You may have more luck in the Mechanics section.

^^^what he said

cassettes are tight and i have used multiple cables through the process

could it be the return spring is worn? No longer has the strength to pull, or cable is binding.

I doubt the spring is worn, the groupset only has about 3months and 1200miles on it. I dont think the cable is binding the shifting action feels smooth if i hold the cable taught with it not attached to the rear derailleur but through all the housing.

Check the cable routing at the rear derailleur. Be sure that the cable is on the correct side of the fixing screw.
Are you sure the derailleur hanger is not bent?

You've replaced cables, but have you also replaced housings, especially the rear loop. Also is the loop the right length? By right length, I mean so that it meets the RD adjuster perfectly in line.

yup all these things are good

housing is the correct length, but I don't understand why all of a sudden sram would be so finicky even if the loop was off by just a bit. I am certainly not perfect at doing housing but sram was never the type of system to need perfect cable routing.

Did you check if the rd hanger is straight??

In some bikes when you tight the quick release too much the hanger tend to twist just 1 or 2 mm and that could be your problem.

Good luck.

You have tried a lot of things there.
Stiff chain link? Remove the chain and try each one for freedom. Check the joiner link when you put it back on.

Is the chain the right width? A 9 speed chain on a 10 speed cassette frinstance will give you grief - if it were to work at all.

Chain length - I use chain checkers - don't mention them in the mechanics forum whatever you do! Measure with a ruler to be absolutely sure. For reasons which I finally understand but take too long to explain - the Shimano style checker is the only reliable one, but a ruler is failsafe.

The remaining common factor seems derailleur hanger alignment. The only way to do this well is with an alignment guage. Since I bought mine pretty well every bike I get is out of line until I tweak it. Sometimes it makes a difference, not always, but sometimes. Don't bother checking by eye - you will only see what you think that you should be seeing.

Test your shifter by pulling on the cable to simulate the return spring load - shift up and down. Try with a light pull and see if the shifter internals are working properly - sometimes the work ok but only with a heavier pull than the derailleur is providing.

Another thing to try is - can you shift gears up and down by pulling the cable yourself (not with the shifter). If you can then this points to the shifter being erratic.

Sounds like you have a lot of experience so the following is not likely but I'll mention it anyway: Sometimes the housing gets pulled away from being fully seated the shifter when taping the bar. This allows it to move and contribute to inconsistent shifting. This is less likely when routing the cable behind the bar. FWIW, I tested routing the housing in front and behind the bars and found that routing behind, as you do, created less cable drag.

Are you trying to use the "little-little" combo? If so, maybe want to not do that.

I had a similar mystery shifting issue on my bike last year. I still remember when it started. For a long time I was sure it was the derailleur hanger but multiple attempts to align it never quite corrected it. I even found a broken piece of metal in my right 7900 shifter which Shimano warrantied but that still didn't fix the issue. I replaced cables and housing, I tried adding more Shimano SP-41 grease, and even repeatedly inspected the BB cable guide. The final fix was that my damned rear loop was too short.

What's the frame? Horizontal dropouts? Where in the dropouts are you clamping the wheel?