Attaching rigging wires to a wing prior to putting the wing in place can lead to stress.... but in my experience is the best way forward. Bad luck with the mis-aligned strut and the ones which would not fit properly. I always hesitate when deciding whether to prefabricate or build in place and I usually go for the latter because no matter how careful we are, something will not line up properly, or there will be a measurement error.
Good for you for taking the trouble to correct the errors too - you will now be able to look at the model and not think about them!
Stephen.