Getting the machine to run smooth with 020 and OS3.9 will meen cutting back on most of the bells and whistles of OS3.9 though.
Wrong. 3.9 ran fine on my A500 with Viper 520 - even using the slow A500 3.1.
You can plug the A1200 3.1 ROMs in the Viper 520 3.0 ROM slots - if you're an expert at soldering. I bought the A1200 3.1 ROMs to do this, but got too scared to actually do it (no, I'm not a soldering expert). One false move and you're sitting there with a $300 pile of junk and a stock A500! I was thinking of taking it to a professional service, but there's no guarantee that they won't fry it.
I suggest you keep the 3.0 ROMs and use WB 3.1. 3.9 is overrated anyway and has no improvements for an A500 other than HD > 4Gb and this can be done in 3.1 using loadmodule. Even if I put the 3.1 ROMs in the Viper, I'd still use WB 3.1 instead of 3.9.
If you need any help with fixing up WB 3.1 on your A500, I'd be happy to help. :-) (..see my A500 WB3.1 screenshot:
http://www.amiga.org/gallery/photo.php?lid=2175 )