You have a similar machine to mine. A3000 16/2MB. A3640 68040/25. GVP spectrum RTG card. Subway USB. Elbox Fast ATA controller. X-Surf network card w/ clock ports. I too run 3.9 and it is an OK experience for the most part. I remember the first time I installed each piece of the extra-curricular hardware and saying 'wow, who would have thought an Amiga could do all of this?' Now I am thinking of reconfiguring the machine to just perform a small set of tasks, thus a lot of the modern stuff can all blow away in my opinion.
As far as going to an operating system from the Commodore days, WB3.1 would be a good choice in my opinion. I have become very intrigued by the BetterWB software package. It contains many very good things that will give WB3.1 excellent functionality and it should not instill heavy system demands.
This is the route I plan on taking with my machine. I am tinkering with OS/software configurations in UAE at the moment so I can be best organized when I do it on real hardware.
Best of luck!