As for getting her respect/confidence, if she is best with you I would be having only you working with her for now until she gets more confident, then start introducing your wife into the equation again.
One part of Parelli that I DO agree with, is the basic foundation of the seven games. Not all of them though. To some extent.
I'd be doing what he calls the 'friendly game'. Spend time with her in the round yard, maybe just sit and read a book etc. Let her get used to you being around her and let her realise that you're not going to jump out at her and try to make her do things every time you approach her.
Once she's comfortable with your presence and will approach you, start stroking her. You want to be able to touch her everywhere without her flinching or moving away. So start in the areas where she is most comfortable, maybe her lower neck and shoulder? Gently rub her in circular motions until you fell he muscle relax, then move across her back, her front legs, under her girth, hind quarters, hind legs, tail etc. Doing both side of her body. Because she is so head shy I would leave her head until last.
Give her a good week or so of doing this, it will make her realise that you're not out to get her, and being near you is actually quite pleasurable.
When she is happy to be around you, start asking her to move away from pressure. Backing up is one that I like to teach first as it is a very usefull aid to have on the ground- it has stopped me getting run over many a time! Stand a little to the side of her and put a couple of fingers against her chest, and push, walking a little towards her. As soon as she takes a step back, take the pressure off and rub her chest. Then ask again. It won't take much to get her backing up on command, and then you will be able to use that to stop her from running you guys over, just walk towards her and prod her!
From backing up, I'd go to walking forward from halter pressure. Put a halter on her (I prefer rope halters for horses like this as they give a more direct pressure on the poll, jaw and nose so that you don't need to use so much force to get a reaction) and standing just in front of her shoulder, put some pressure on the lead rope (pushing to towards her nose, so that the halter pulls a little on her poll/jaw) and she SHOULD move forward from that. If she doesn't, she not sensitive enough. Carry a crop or a dressage whip with you, and if she doesn't go forward from a slight pressure on the halter, tap her behind the shoulder. Be aware that she may jump forward so don't catch her in the face with the halter as any forward reaction is a good reaction to start with, you can fine tune it later.
When she is going backwards and forwards off slight pressure, move onto sideways movement. Basically where ever you touch her body, you want to to yield. So if you touch her jaw, you want her to turn her head, touch her shoulder and she should cross her front legs, touch her girth and she should bend away from the pressure, touch her hind quarters and she should cross her hind legs etc etc.
Yielding the hindquarters is probably the easiest to teach from what I've found so far, so start there if you feel comfortable. Make sure that she is comfortable with your being around her hindquarters by playing "the friendly game' a little there, rubbing her over the hind quarters and stifles until she relaxes with you being back there. Standing to the side of her hind quarters (safest spot is actually close to her hindquarters level with her back leg- much less damage if you get kicked from close quarters if she decides to have a go!), put a little pressure on with your fingers/fist round on the side of her rump ask expect her to move over. If she doesn't move, or leans into you, increase the pressure and if that doesn't work, small jabs will usually stop them being ignoranent and they will move across. Every time you do this, start with the smallest pressure first, and as soon as she steps across, take the pressure off and rub her.
Same goes with other parts of her body.
Essentially, you want to be able to touch her anywhere and move her anywhere. Once she understands this, you will have yourself a horse that is so much safer and more enjoyable to be around, and she will enjoy your company so much more as she will understand her job.
When you reach this point with her, start introducing your wife into the equation, getting her to go through the same process.
I would be doing this work before trying to bridle her and ride. When working with new/timid/green horses it is always best to take things slowly and build there trust step by step. It will make for a longer and more enjoyable relationship ;)