I am a bit puzzled on how to set this up. I turned the screw inwards a little bit until it makes clicking and then back off a bit. I found it difficult to visually line it up, soundwise it always make a bit of extra noise in the smallest cog. I also wanted to make sure it upshift smoothly when dropping the smallest cog and not hesitate.

So in the end it seems the best setting was what seemed slightly outboard below the cog. It takes a bit more for the chain to drop out of the cog, right?

Try and line it up so that both the teeth from the highest cog and from the upper jockey wheel are rolling through the middle of the chain. It can be hard to tell sometimes visually though. I also turn limit screw in until it starts making noise trying to go to the next cog, then count the number of limit screw turns it takes to go from there to the opposite side where it starts making noise going towards the frame. Then turn it back it half the numbers of turns you just did and it always gets me dead on. Sorry if the wording is a bit convoluted.

It's a lot easier to line up the jockey wheels and the sprocket when you don't have the chain on.

of course I did at first but when I put the chain on it makes the clicking, so I am probably blind or something

Also, when the chain is under load the alignment can vary compared to on the workstand. Try it on a turbo.

I did the same thing.

I've done much harder things in my life (converted a car from auto to manual, built an engine, welded a full exhaust system)
and so far my damn rear derailleur with 3 screws on it is beating me.

At first I removed the chain to visually set my high and low...but as soon as the chain was on it started to interfere...so i just went by a mixture of sound and visual guessing.

I may set them again tonight just to get myself more frustrated.

I do the following:

1) Align it without chain to get close. 2) Install chain and pedal in the stand. 3) Tighten high limit until I hear clacking noise. 4) Loosen high limit while counting turns on the screw until I hear clacking noise on the other side of the cog. 5) Tighten high limit back half the amount of turns counted.

Seems to work well on Campy and Shimano systems with either an 11 or 12 T rear cog.

That seems to make sense to me.
Someone told me I need to release the tension on my barrel adjuster first. Do you do that?

And how do you do the low limit setting?

you can adjust the high limit without a cable attached. if one is attached, make sure that the cable has some slack at all times during the high limit adjustment.
then you anchor the cable, shift easier/harder and adjust the cable tension until indexing is good.
then shift to the largest cog, screw the low limit in until the chain makes noise. back off limit screw just until chain does not make noise. then test by shifting to second-easiest cog, then back to easiest cog. if the chain goes to the easiest cog quickly, youre set. if it struggles, back off limit screw 1/8-1/4 turn and retest.
also, when in the easiest cog, and you push the shifter to shift easier again, the derailleur should not be able to move to the spokes any further (except with sram road, just a tiny bit).

Here is some REQUIRED reading:
http://m.parktool.com/blog/repair-help/ ... derailleur

http://m.parktool.com/blog/repair-help/ ... -alignment

EM3

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My 2011 Cervelo R5

I just used this and worked great. It does make a little noise when it is too far outwards. Then I divided by 2 and turned the screw half the turns in between.
The hesitation I had when dropping to the smallest cog is gone.