+1 I would pickup a Indivision AGA unit. It makes a big difference on modern LCD monitors even widescreen ones. CRT would be good for retro scanlines but definitely LCD would look better.
From my understanding its best to only try OS 3.9 if you have a 060 or better accelerator. OS 3.1 what you have would be the fastest option. Best to get another CF / main drive and try perhaps try out OS 3.5. Nothing would stop you from trying within WinUAE which would be more powerful for OS 3.9 up.
060 accelerators are very pricey.
I would grab a 030 accelerator or one of those ACA accelerators.. Much cheaper and OS 3.1 goes pretty fast with it along with whdload.
Heres other peoples experiences with OS 3.9 on various hardware specs.
http://www.amiga.org/forums/showthread.php?t=61127 Non accelerated Amiga is reported as Choppy experience.