How can I get java popups to open in tabs

I teach online, and our courseroom software has the unfortunate design of opening everything - student discussion posts, links to online articles, documents and forms, links to our university website or to external sites - in pop-ups via Javascript. This is a superbly annoying "feature" and contributes greatly to repetitive strain as I am constantly having to drag and re-size windows so I can read them. Also, the Java is coded such that I cannot pop open multiple items and let them load - each subsequent one loads over the top of the one previously opened. This reduces my working speed enormously, since parts of our servers get taxed and load quite slowly at times.
For some time now I've been trying to work around this as best I can by allowing a pop-up to load, then copying its direct URL, closing the pop-up, opening a new tab, and pasting the URL in. At least this way I can get several items loaded that I can switch among. But again it creates tremendous repetitive strain.
I thought I had worked around the problem by going into about:config and setting browser.link.open_newwindow.restriction to 0 rather than to 2. This did cause a pop-up link to load in a tab. However, it didn't solve the problem of subsequent clicks causing the new URLs to load over the top of the previous one in said tab. Instead of each click spawning a new tab, they all just load in the same tab one after the other, defeating the purpose as surely as the pop-ups did (though at least without having to re-size the window.)
What is the solution for this? One quarter of teaching online has destroyed my hands and wrists, after years of pain-free computer use. I'm doing PT and looking into various different equipment but cutting down on the pop-ups would help both my pain and my workflow tremendously. (Firefox can't help me with the terrible Java coding in the main courseroom, that refuses to respect my re-sizing of windows and sidebars and always scrolls you back to the top of a page after popping open an item linked within that page, but I'll take what help I can get.)

As of five minutes ago, ''every single'' link I click opens in a new tab. This includes clicking the refresh button.

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