Upvote:5
Several sets of rules (specifically the Schengen Borders code and the Free movement directive) interact here so it can indeed be a little confusing. A lot of material available online, when not outright wrong, is also concerned with the rules that apply to regular holders of Schengen visas or other documentation (i.e. people who are not married to an EU citizen) but other rules apply to your wife.
While she does need some visa or residence permit to cross the border, your wife is definitely entitled to stay with you in the EU for longer than 90 days, even without any long-stay visa. That means that even if your wife enters the Schengen area with a short-stay visa, she wouldn't be doing anything illegal by staying longer than 90 days (as long as she is travelling with you, an EU citizen).
Technically, you might need to register or otherwise prove you qualify for residence and then apply for a residence permit for her if you stay in any one country for longer than three months but there is no such requirement if you move between countries within the EU/Schengen area.