Hello
A long time ago i had also an Amiga4040/25+16Mo and a CV64/3D --> Shapeshifter was working fine & fast so i didnt use anymore my real Mac 68040
Badly i dont remember the configuration but it was something very simple in this RTG case (I mean i wasnt using an exotic external driver as the Mac hit directly itself in video ram)
Perhaps it will help here it is my config in ShapeShifter/WinUAE
ShapeShifter: Graphics settings
1 Monitor
24 bit (16 M colors)
Screen Type: CyberGfx/P96
External driver: [empty]
Screen Mode: 1024*768 32bits
Sive 1024*768
refresh rate 1
Black border: [empty]
Refresh always Yes
MMU refresh: [empty]
Amiga Mouse pointer: [empty]
Alain Thellier