Travelling in Europe after Brexit as the spouse of an EU Citizen

We realise that we require a visa to stay in Spain for more than 3 months in one visit (long stay)

You do not require a visa, nor does your wife as long as she is with you.

However, I believe that the 90/180 day limitation does NOT apply to me and my wife when travelling in the Schengen zone together, because if the non EU spouse is regulated under the 90 days in 180 day ruling, the EU would be restricting the Freedom of Movement of the EU spouse.

That is correct. In fact, the definition of "third-country national" in the Schengen Borders Code actually excludes family members of Union citizens who enjoy freedom of movement. If anyone points you to a provision in the Schengen Borders Code, therefore, in support of some claim about the 90/180 rule, you can point out that this doesn't apply to your wife because of Article 2(6) (see below).

However, if you stay for longer than three months in Spain (or in any Schengen country) your wife can be required to apply for a "residence card of a family member of a Union citizen." I do not know what penalties Spain imposes for failing to apply for such a card, but they should be "proportional," meaning they should not be terribly severe (for example, in France you would risk an extra application fee of less than EUR 300). In any event, the penalty cannot include expulsion.

Note that this three month period is per country, so it doesn't apply to the Schengen area as a whole. On the other hand, it's possible that a trip of a few days outside of Spain might be seen as not interrupting the period of residence. It would be safer to apply for a residence card than to try to play such games.

For reference, here's article 2(6), with emphasis added to the relevant portion:

6. ‘third-country national’ means any person who is not a Union citizen within the meaning of Article 20(1) TFEU and who is not covered by point 5 of this Article;

For further reference, here's article 2(5), again with the relevant portion emphasized:

5. ‘persons enjoying the right of free movement under Union law’ means:

(a) Union citizens within the meaning of Article 20(1) TFEU, and third-country nationals who are members of the family of a Union citizen exercising his or her right to free movement to whom Directive 2004/38/EC of the European Parliament and of the Council applies;

(b) third-country nationals and their family members, whatever their nationality, who, under agreements between the Union and its Member States, on the one hand, and those third countries, on the other hand, enjoy rights of free movement equivalent to those of Union citizens;