Hi, replacing the wine folder is OK. You can always replace it with older version of wine to see if it makes any difference with your font issue.
What's your Mac resolution and what is the resolution of your AmiKit?
If you run AmiKit in full-windowed mode, try to switch to full-screen or windowed mode. Press F12 and in WinUAE go to Display and change the RTG settings accordingly.
Then, if Workbench fonts are displayed OK, you probably have to select different screen mode for AmiKit when running it in full-windowed mode. Press F12 and change the RTG mode back to full-windowed. In AmiKit run AmiKit:Prefs/ScreenMode program and test some other screen modes to see if they look right (but always choose 32bit BGRA modes).
Hope it helps.