Ok, I hope you're familiar with stacks and cache.
This is the method that I use:
1.- You must have an mp3 (Wav in your case) stacked to the original flac. You can do this with a handheld and cache enabled. I do it with an smartlist to check which of my flacs don't have stacks, and a handheld to stack automaticaly. If you have questions about this please feel free to ask
2.- Create a special view where you see the files you want in your iphone, this will include lossy files (mp3, m4a) and WAV files that are stacked to the flacs (the flacs should not appear there, only the wavs) If you need help to set up this view, again feel free to ask.
3.- Export to itunes and iphone that special view.
Btw, MC 18 will have alac encoding so you will not need wav in the future