I am getting a CRS score of 390 whereas my wife scored 431 because she has more than 5 years of experience under one NOC which matches her roles and responsibilities in her current and previous organisation.
Just wanted to check if my wife can apply separately for FSW under EE and I can apply separately.
It is possible. Both of you will have to declare each other in your respective application.
Recommend that you create only 1 profile with your spouse as PA. There is no way the cutoff will fall below 400 and, even if it does, your wife's profile will get an ITA much sooner than your profile.
Make sure when you are making the profile with your wife as PA, you mention your status as 'accompanying' spouse.