What Tony describes about link lengths combined with 90° servos is correct, and this would give you a level swash - in a perfect world.
My personal recommendations regarding 3GX set-up:
This should be done in the 3GX DIR mode (throttle hold engaged).
Center Tx sticks.
If servos are not perfectly 90°, use Tx sub trim.
If you have to apply lots of sub trim, try swapping servo horns around.
A value above 40~50 of sub trim is not optimal. The less sub trim - the better.
At this point servos should be perfectly 90°.
Link lengths should be according to Aligns instructions.
Use a swash level. If you do not have one, use the zip tie trick (not optimal but works - sort of).
Adjust servo link lengths until you get a perfectly level swash.
It shouldn't be necessary to adjust a lot.
E.g. if one link is much higher than the other two, lower IT one turn and raise the OTHER TWO one turn as well.
Reason and logic should be used when doing this.
Your swash should now be perfectly level, with servos at 90° at Tx mid sticks.
Never mess with the sub trim again, as you would have to redo all these steps.
Adjust your pitch link lengths according to Aligns instructions (the links which go from swash to blade grips).
Put on your pitch gauge.
At Tx mid sticks you will want 0° pitch.
If you now have positive or negative pitch, increase or decrease pitch link lengths until you get 0° pitch.
Remember to adjust both links, they should always be the same length.
When you get 0° pitch, you want to check your collective pitch range.
Give full positive pitch on your Tx (left stick up) - check the value.
Give full negative pitch on your Tx (left stick down) - check the value.
These two values should be the same.
E.g. you can have +18° positive, and -18° negative (these numbers vary).
But you may also get +20° positive, and -16° negative (this is often the case).
It's hard to get the exact same value, so a 0.1°~0.9° difference is acceptable.
If you got uneven values you will have to correct.
This is done by raising or lowering the swash mechanically (adjusting swash link lengths).
Raising the swash will compensate for too much negative collective (e.g. you got +16° and -20°).
Lowering the swash will compensate for too much positive collective (e.g. you got +20° and -16°).
Adjust all three swash links one turn at a time (remember A's outside).
When swash is adjusted, you'll need to readjust the blade grips again to achieve 0° at mid sticks.
This process takes time, and needs some good old trial and error the first time.
You should now have 0° pitch at mid sticks, servos 90°.
You should have matching values for positive and negative pitch (e.g. +16° and -16°).
Your head is now perfectly set up.
Next is to decrease or increase collective range. This is done in your Tx "SWASH MENU".
I'll not get into that right now, but it has to be done before completing the 3GX DIR set-up.
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Tail set-up.
This should be done when you have finished the 3GX DIR set-up.
First go into DIR mode.
With left stick centered, your tail pitch slider should be mechanically centered on it's slider.
If this is not the case, you will have to adjust the tail pitch control rod.
When you've gotten the tail pitch slider centered, exit DIR mode.
There should be NO sub-trim in your Tx rudder settings.
The rudder servo travel should be 100%-100% (default).
No messing with Tx endpoint set-up.
Go into the 3GX tail set-up (hold 3GX button until LED's change).
Scroll through the steps until endpoint set-up.
First apply left rudder until rudder servo starts to bind (buzz), then right rudder slightly until binding seizes.
Hold there until the blinking 3GX lights blinks RED once.
Then immediately rudder right until servo binds, rudder left slightly until binding seizes.
Wait for the blinking light to blink RED once again.
Press 3GX button a couple of times till you exit 3GX rudder set-up.
To confirm rudder is correctly set-up.
Power on bird with throttle hold engaged (bird stationary on work bench or whatever).
Rudder far right, there should be no binding.
Rudder far left, there should be no binding.
If there is binding (buzzing) redo rudder set-up.
This concludes rudder set-up.
- - - Updated - - -
There may be inconsistencies in this write up, as I wrote it right of the bat.