If WinUAE is slow, then it's your configuration, not the OS. On WinUAE there is no difference between 3.9, 3.5 or 3.1. Everything runs incredibly fast.
Use the latest WinUAE (1.5.3), select "UAE expanded configuration" from the Quickstart menu, increase RAM to convenient settings (for example 8 MB Chip, 256 MB Z3 and 32 MB RTG), then install OS 3.9 onto a HDF and install Picasso96 and AHI with appropiate drivers for UAE. It will run unbelievable fast compared to a real Amiga.
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