Your procedures were exactly correct.
Lock the outboard end of the aileron with the template, lock the bellcrank with the pre-set push tube, center your sticks, then adjust the long push rods. Like Pierre said, now lock the ouboard ends of the flaps to the ailerons and then adjust the overhanging flap skin to the fuselage( bend up, or joggle down). Then I install the wingtips. Put the flaps up, lock the ailerons to the flaps, and adjust the wingtips so that the trailing edge aligns with the outboard aileron trailing edge.
IF YOU DO IT THIS WAY, YOUR AIRPLANE WILL FLY STRAIGHT WITH THE STICK IN THE NEUTRAL POSITION. ALL THE CONTROL SURFACES AND THE WINGTIPS WILL BE ALIGNED.
THERE MAY BE SOME WING HEAVINESS BUT THAT USUALLY CAN BE CORRECTED BY SQUEEZING THE AILERON TRAILING EDGE.
This prodedure has worked for me on 6 planes now.
The digital level is great for leveling the plane and maybe for setting the incidence angle. Otherwise it will only frusrate you.
If someone has managed to build contol surfaces without some slight twist or curve in at least one of them, my hat is off to you.
The aeronautical engineers out there can debate this all they want, but these steps have worked for me and I have never adjusted the rod end bearings of any of the control surfaces after the initial control rigging.
The aileron squeeze/or unsqueeze has always worked to make the plane fly hands off.
I would throw my digital level away, but it comes in handy for other things.