Hey Rusty:
I know that the thing you least want to hear after you've glued in a part is a better way to align it, but -- I'm compelled.
I put my wings in to be square with the fuselage, not with the motor. You can do this with a tape measure and some patience, and get a superlative job every time. Here's how:
First, pick a reference point on the wing that's the same from side to side. In your case, the corner of the outboard rib and the spar is probably a good place. You want to define a point that you can always come back to, and have it be clear where it is both side to side and fore and aft. If you're building a plane that has an asymmetrical wing, make a witness marks on the spar that are the same distance from the fuselage, and as close to the shorter wing's tip as you can.
Second, it's good to arrange the aircraft so that you can get the wings located to your satisfaction and then glue them on without disturbing anything. I can't remember who taught me this (it was someone here), but a good way to do this is to file some half-round notches in the wing mounting hole, about 1/8" to 1/4" in diameter, and four or five each on top & bottom. Make them just deep enough that you can inject some epoxy in there with a disposable glue bulb. That's really all you need to hold a wing in on most planes, but if you make your fillets out of epoxy or wood that'll add a huge amount of strength.
Now put the wing in the plane, and measure it from side to side. Get the wing jiggled into place so that the measurements are as close to equal as you can get them.
Now choose a spot at the tail end of the fuselage that's dead in the center (you want a straight fuse for this). Measure from that spot to each of your witness marks. If these two measurements are correct and if you didn't knock your wing out of center, then your wing is dead square to the fuselage.
While you're doing all of this, you should have your wing propped up on the building board so that it is level spanwise, and so that the fuselage sides are straight up and down. If the wings are a bit tight in the wing hole and everything is square and centered -- lucky you! If not, then sand, cut, pin, shim, tape, or whatever until you get it square and stable. If it's binding a bit and you have to put a brick on it to get it square, take it apart and correct the bind.
Put it together and measure again.
Measure again (no, that's not a typo -- "measure twice, cut once" is for when you have a saw in your hand. "Measure lots, glue once" is the companion aphorism).
Go away for a bit. Come back. Measure again.
Take a deep breath. Mix up the slowest cure epoxy you have. Put your can of lacquer thinner or 99% denatured alcohol on your bench, just in case. Glue in the wing (I use those little squeeze bulbs, injecting glue into those notches I was babbling about. You can also pull the wing out of the fuse a bit, slather on some epoxy, and then slide things into place -- but you have to disturb the wing-fuselage joint if you do it that way).
Now measure again, and again, and again. If for some reason you can't get it straight then rip it apart right now!!! -- scrape off the glue before it hardens, take a rag or paper towel and that solvent that you left on your bench and wipe off the rest, then turn out the lights and stomp out of your shop until you stop shaking (and the glue that's left sets up).
If you didn't have to rip it apart, then measure it one last time, secure your work area from curious children and pets, and let the glue cure. I always come back and measure once more after the glue is set, even though I know that it may lead to heartache.
I do more or less the same thing with horizontal stabilizers, except then the most important thing is to get it square and level with the wings -- if the wings are a bit cockeyed to the fuselage, at least get the stab straight to the wing.