Here are some things that can cause differences in flipper strength when all parts are new, besides what you already mentioned.
If you haven't done this yet, you can check your coils (out of circuit) with a multi-meter to see how many ohms you have on the power windings. If the ohm reading between the two coils is much different, the one with the lower ohm reading will generally have the stronger kick.
If the return spring tension is different on the two flipper assemblies, the flipper with the stronger return spring will have a weaker power stroke.
If the plunger pivot on the flipper crank is binding on one crank but not the other, the crank with the binding pivot will seem weaker (yes you can have a binding pivot on a brand new crank).
If the flipper crank is installed on the shaft of the flipper such that the bushing of the crank is too tight against the bottom end of the nylon sleeve that runs through the PF, that binding point will make the flipper weaker. If one flipper has good end-play between the crank and the sleeve bottom, and the other flipper is too tight, then the tight flipper will seem weaker.
If the coil mounting bracket for the flipper coil is positioned such that the plunger path into the coil is not lined up quite right, the plunger can bind against the inside wall of the coil sleeve. This mis-alignment can sometimes be caused by attaching the flipper crank onto the flipper shaft too far down (ie, towards the end of the shaft). If one flipper plunger is binding in this way and the other isn't, then the binding flipper will seem weaker. You may not notice this type of binding problem unless you check the action of the flipper assembly while the PF is in the normal playing position.