How isolated were Yemenite Jews in the last millenium?

Your question is difficult to answer because "how isolated" is very generalized, particularly since you have not specified who they might be isolated from. However, during the period in question, the Yemenite settlement was not entirely isolated from the large Jewish community in Egypt:

The Epistle Concerning Yemen:

An even more famous letter by RAMBAM (Maimonides) Epistle Concerning Yemen.. this epistle was written in response to a query by a Yemenite sage, Rabbi Jacob al-Fayumi during a period of violent persecution and religious intolerance in his country. About the year 1168, the Jews of Yemen were confronted with a three-pronged agonizing problem....Rabbi Moshe ben Maimon addressed a letter to this sage, and through him to the entire Jewish population of Yemen.

RAMBAM was apparently living in Egypt at that time, where there was a large and vibrant Jewish community: Following this sojourn in Morocco, together with two sons,he (RAMBAM) sojourned in the Holy Land, before settling in Fostat, Egypt around 1168. So apparently there was communication and exchange between the Yemenite Settlement and that of Egypt.

Further, during the period in question, the large Jewish presence in Yemen, had contact with other Jews, during the periods of Ottoman Rule:

From the 1200s to the 1600s, the hardship of Yemenite Muslim rule was brought to a temporary halt by the Rasulides, a tribe from Africa. In 1547, the Turks took over the region from the Rasulides. This allowed the Jews a chance to have contact with the Kabbalists in Safed, which was a major Jewish center at that time.The Yemenite Jews were also able to connect with other Jewish communities under Ottoman rule....In 1872, the Turks took over Yemen again and the Jewish condition improved. Just like with the first Ottoman rule, Jews were allowed more contact with other Jewish communities. They were also allowed to practice their religion more freely.

In general, throughout the entire period, Jews were a constant presence in Yemen, and Yemen itself was by no means an isolated place:

• Major tribes, including Himyar, sent delegations to Medina during the Year of delegations around 630–631 AD. Several Yemenis accepted Islam before the year 630 like Ammar ibn Yasir, Al-Ala'a Al-Hadrami, Miqdad ibn Aswad, Abu Musa Ashaari, Sharhabeel ibn Hasana and others
• The country was stable during the Rashidun Caliphate. Yemeni tribes played a pivotal role in the Islamic conquests of Egypt, Iraq, Persia the Levant, Anatolia, North Africa, Sicily and Andalusia. Yemeni tribes that settled in Syria, contributed significantly to the solidification of Umayyad rule, especially during the reign of Marwan I. Powerful Yemenite tribes like Kindah were on his side during the Battle of Marj Rahit. Several emirates led by people of Yemeni descent were established in North Africa and Andalusia.
• Yemen was held by the dynasty until a deputy governor proclaimed his independence from them in 1229 establishing the Rasulid dynasty. During the next two centuries the Sunni Rasulid sultans governed a strong state that also encompassed Hadramawt. In 1454 they were superseded by another Sunni dynasty, the Tahirids. Contemporary with these regimes was a series of Zaidi imams who ruled in the northern highland, usually in opposition to the lowland dynasties. The Tahirids held sway until 1517 when they were defeated by the Mamluks of Egypt. In 1538, the forces of the Ottoman Empire absorbed Aden, and between 1547 and 1548 they conquered Sana'a and the highlands.

Since Jews were present and actively involved in Yemenite cultural and economic activities throughout this period, and historically Jews always did what they could to maintain business and religious connections with Jews in other locations, it appears safe to assume that the Yemenite Jews were never entirely isolated from other Jewish settlements in Arabia, North Africa, and the Middle East at large. Still, it does appear that during certain periods they were more "connected" than at others.

If you are asking with respect to a Yemenite connection with European Aschenazic Jews, the answer would be that there was minimal contact between these groups, although I have not done the research now. I can only answer based on my personal knowledge as an Israeli: The first significant connections between European Jews and their Yemenite brethren were only established after both groups arrived in modern Israel. Beginning in the 1950's (By 1950 almost all of the Yemenite Jews had relocated to Israel) and extending until today, in modern Israel Yemenite and European Jews interact and share a great deal, socially, culturally, economically and religiously, although each group maintains its own religious and cultural traditions and identity.