I read the first couple pages, but then skipped to the end, and saw this. All I can say is, "WTF?" And that's directed to you, not her. Are you married, or what? if you're married, what the hell is with accounting for what you paid for, and needing to be "paid back"? You're either in it or not.
I can see and understand your disgruntlement with your spouse's putting the inheritance money in a separate account. But whether it's logistically "right" (whatever that means, according to Flagpole), this isn't some lottery she won, or a bonus from work. It's an inheritance from her PARENT and is likely weighted with all kinds of emotional baggage that distorts any conception of what's "right" and "wrong" from a "we're married so everything is OURS not YOURS" point of view.
If you're more than 12 years old, you should be saying, "God bless you my dear, I'm sorry your dad died. Do whatever you want with the money, because I trust you." Forget about it and move on. You're either in it for the long term (in which case the identity of the bank account holding the money makes no difference), or you're not (in which case you should quit complaining and break it off now).
Good luck, and I mean that.