I'm experimenting with AmigaOS 4.1 FE through emulation before comitting to specific hardware. WHDLoad allows me to run games from an OS 4.1 Hard Disk but doesn't alter the runtime performance.
It sounds like you're probably at the limits of what the emulation can do on your hardware.
If you have an old CRT monitor tucked away that you can hook up to your hardware then you may be able to run a real 320x256 or similar resolution if Windows allows it. If not frame skipping may improve the experience in a less than ideal way.