I run OS 3.9 + BB1-4, Visual Prefs, Peter K.'s icon library, and the Rebel palette on my A2000 using Indivision ECS and a LCD monitor. I typically run either 800x600x16 color SuperPlus, or a custom 700x482x16 color screen mode (is a little faster than SuperPlus). Attached are a couple screenshots of my system that I took a few days ago. While I'm still in the market for a graphics card it's a low priority, given the cost. Honestly I've shown this system to people and they're shocked that it's only 16 colors. 
So, yes, 3.9 will absolutely run for you on the Indivision ECS. :drink:
That is one of the best 16 color systems I have ever seen! Great job Mike, that is a sweet system.
