About 5 years ago we switched 4 site over to Joomla 2.5 from 1.5. When we did this they wanted to change up the category structure. We also established SEF URL structures getting rid of article Id number and suffix in the URLS. the last article published with the old URL was in 2012. BUt google is still crawling those URLs. Are these old URLs still in the sitemap I Create in Jsitemap? It has been so long I am surprised that they are still being indexed.

Are these old URLS (news articles by the way so really "old" news and not visited very often or at all.) going to affect our SEO rank? We are currently PR5 and I would like to get higher than that.

Any help would be appreciated, I am very much a novice in this whole SEO ecosystem.

I can't answer you without a deep analysis of your website and detailed informations about links you are talking about.
However there are 2 aspects to mention: you can't have links to article without the id number in Joomla, unless you link each article to a different menu item or you are using an extension such as sh404sef.

PR5 = Page Rank? The Page Rank is dead, it does not exist anymore.