Just chill, you're doing better than you think
Honestly, I think that you're more worried than you need to be here. While there are obviously a few things to work on moving into the future, it sounds like you and your wife have a pretty strong relationship. It sounds like you've talked about the stuff that seems to be problematic (her lying and you spying) and resolved the issue/s (by agreeing not to do that crap from now on). This level of honest communication is awesome, and I think that if you continue to be honest and open with those you are involved with, things will go well for you.
From where I sit, it sounds like the only thing that's actually left on the table is GF's reaction to your spying (which you told her about honestly <--AWESOME). Really, I don't think you have too much cause to be worried. Assuming GF's a reasonable person (and if your wife loves her, that's a safe bet I hope?), I think that your communication with GF will yield understanding, forgiveness, and solutions for the future.
Keep up the good work (honest, open communication) and, seriously, these kinds of issues will come to pass, strengthening your relationships as they go. They'll never feel great, but these little speed bumps are just that: little, as long as everyone is talking and making an effort to resolve current issues and avoid (as best they can) continuing non-constructive behavior.
Me: Straight male, anarchistic polyamorist, hate labels
N: Straight male, best friend throughout childhood
M: Bisexual female, introduced her to poly
C: Bisexual female, 'girlfriend' of N before poly encouraged de-labeling
A: Straight female, newest in my life
I love them all.