OS 3.1 or 3.9

[Oldsmobile_Mike]

No point in getting 3.5, honestly I'm not sure why anybody runs it. 3.1 is good for low-end systems, 3.9 requires a more high end system. Has more eye candy, requires less patches (although still quite a few), etc.
 
What's the exact spec of your system and what do you intend to use it for?  You still rocking the Derringer or going to trade up?  
 
AFAIK 3.9 requires a CD to install, although there might be some way to install it via a USB, or if you were somehow able to copy all the files to RAM:, or if you prep a CF in WinUAE, may be a work-around.

[Oldsmobile_Mike]

Would you have any pics with the Indivision ECS installed but without the bracket PSU tray installed? I wanted to see which way it is orientated. The Derringer does not fully cover the Denise chip.

Yes, I posted them in the previous thread, five posts down, here:
 
http://www.amiga.org/forums/showthread.php?t=66479&highlight=amiga+2000+indivision
 

 
 
Otherwise your system specs sound fine for running either version. I'd try to bump up that chip memory to 2MB and get the CD drive working first, obviously. On the bright side once you've got it working right, CD support under 3.9 is much better than previous versions (i.e., you don't need AsimCDFS or anything like that, no problems with filenames longer than 8.3 when copying discs from Windows systems, etc.)