IMO, sdn40, the large diameter tubing plays to your modern graphics idea, which I think could look pretty sweet. Since Cannondale kept the large tube and traditional geometry (read: horizontal top tube) for quite some time, and still mostly does it today (at least one model will keep it close), you have many years of graphic schemes to take inspiration from.
Vintage Cannondale has reproduction decals and since you aren't picky about year-specific decals (fonts, mostly, in Cannondale's case), then take a look at these. Multiple color options to choose from as well. I would work with those (types of) choices and let the paint color play off of it. That or nail down some graphic ideas and a place that would be willing to make them, and then go for the color.
What components do you have in mind for the bike? With the Fulcrum wheels it looks like you'll be going with a modern drivetrain (8-11 speeds), so employing some bolder colors could really work. Don't know if you have a favorite color, a color you've not had on a bike, or whatever.
I like your modern stem idea. I did it to my bike (pictured below) and it brought it many years ahead in looks, to me anyway. The recipe was 1) quill stem to 1 1/8" stem adapter, mounted low 2) 1 1/8" stem at 100mm length with a 31.8mm clamp diameter 3) modern short (reach) + shallow (drop) handlebar with 31.8mm clamp diameter. The stem looks properly positioned height-wise with regards to the headset, and its thickness is visually matched by the thickness of the frame tubes. The resulting feel of setup was strong, stiff, yet very comfortable. I like the custom color idea, and I like the modern stem idea!
So for everyone else, I have been holding out on you!! Apologies! She is but a frame again, but during the middle of this year, this was her in her best form. Pictures don't do as much justice to her striking proportion. All that to say, this picture was taken a day after a ride with a friend in which we clocked 44 mph on a long descent. The nearly-75° HT angle and resulting bar setup had her being 100% rock solid stable the entire time. And all other times she was like any other favorite bike--predictable, reacting well to input, etc. Cannondale, as we know, knows their stuff, and certainly did it back in 1989.
