I never ever limit the throttle!
The way I setup any machine, is to fine center on every moving part, all the way up to the swashplate...Then, on the head, I zero the blades, with all mixers level...I check my work by noticing that i have the same pitch , and atv settings lock to lock...
Then I go to the pitch curve to set up what I need while still keeping the curve as linear as possible...
I use a Futaba 9Z, so limit on the throttle is not an issue..I set the throttle linkage by making sure the radio is in default settings with low trim...
I measure the lenght of the ball on the throttle barrel...I use this same distance on the servo arm...I go out one hole for aerobatics, and go in one hole for scale flying on the servo arm...if the engine has no power, I maygo out futher on the arm..
I use a straight wire to center over both axis..With the stick at 50% I use this line to make both arms 90degs ..I check my work by making sure the atv's are the same...
If you have a older JR that has that throttle limit problem..Then after you do all this with the throttle, go to high throttle, take the arm off of the servo...Next go the subtrim, and move it to high side 5 % above what your throttle atv is...You may have to make small adjustments with it, to keep your high throttle setting..So long as you stay 1% above the throttle atv value, it will not overdrive on the swashplate to throtlle mix...
After breaking the engine in, I then deside on the blade

Regards,
Bill Meador,
Team Vario