I'm no expert so just a few notes/suggestions:
- you definitely need an accelerator (or at least some fast ram, but most people agree that 68030 is a reasonable minimum) to run OS 3.9; 4.1 can only be run on "newer Amigas" - A1, Pegasos, Sam440, if I'm not mistaken. The latest version you can run on a classic Amiga is 4.0, but even for that you need a PPC accelerator.
- the compatibility doesn't depend as much on the AOS version as it does on Kickstart version, in my experience there is no difference between 3.0/1 and 3.9 in games compatibility if the underlying HW is the same. With WHDload it is possible to run practically any game on any KS revision, because it uses the required KS version from a file saved on a HDD and fools games this way.
- the maximum resolution you can (reliably) use on AGA is 1024x768, but you need an Indivision scandoubler for that.
- when using bigger HDD you can either create an OS 3.9 emergency disk the OS 3.9 install program and boot with that (and OS 3.9 in a CD drive) and the HD toolbox included on the disk should detect the HDD correctly. Or, if the HDD is already installed and you have some data on it, which you don't want to lose, you can use the fixhddsize util (on Aminet) that will fix it for you.
Somebody correct me, if I wrote some nonsense...
