I've searched the entire internet and come up with nothing, whenever I play this game the mouse flickers and when I move the mouse it causes the game to slow to a crawl. Last time I had this issue (Dawn of War) it was as simple as disabling the hardware mouse in a text document. However I am unable to find any way of adjusting mouse settings in any meaningful way in this game.

Same thing is happening to me, although I suspect you're running this game natively (Windows), rather than on Wine (Linux), which is what I'm doing.

In my case, the mouse flickers both in the menus and also inside the main playing screen, and (even more annoyingly), it actually disappears from view whenever the pointer gets moved, only to show up after about 1 second of being still, so you end up continuously moving the mouse blindly, wait for the cursor to show up, then move again, etc, until you end up with the cursor point at whatever you intended to in the first place. This makes the game completely unplayable.

I've tried using every single version of Wine I could think of (4.21, 5.6, 7.20 (GE), 6.14, 6.16, 6.21, 7.0, 7.1, 7.2, 5.0 (linux distro default)), and changing every single setting I could think of: using "virtual desktop", enabling/disabling CSMT, even fiddling with registry entries that seemed relevant, as documented in the Useful Registry Keys wine wiki article, changing my monitor refresh rate (60Hz and 120Hz), etc., and nothing seemed to work.

I've also tried to find configuration files, and I've looked at [url=https://www.pcgamingwiki.com/wiki/CivCity:_Rome]PC Gaming Wiki's article for this game[/url] searching for clues and tips, but even looking inside the files documented there yielded no useful results.