I only play LN FFA (AOE2 Conquerors Expansion) and when I enter late games (minimum 1 hour 30 min) my game starts to get extremely laggy, screen freezing every 3 seconds.

I have tried re-installing game, and voobly. Neither have fixed this issue

Any advice?

Its always good to do this:
Empty the savegame folders, if you want to keep the recorder games, then move them to another place.
Also delete all files in the multi folder.

Try setting exceptions for Windows Defender:
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And try clearing these folders:
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I've tried those steps and it's still happening. I've noticed during late game I get a fireball icon on all players, it stays for 2-3 seconds then disappears for 10 seconds and reappears, nonstop.... I also get a turtle icon next to my name every few minutes or so..

Did you repeat this step for all game mods?