My beloved 280E had a rough idle when I bought it with 97K miles. I took it in for a major service, and spent about $800 trying to fix the idle. New injectors, various valves, etc. The result was a slight improvement. It still idled lumpily. It also always cranked for a long time when starting warm - not hot or cold. No one could figure that one out.
You will probably never get the idle smooth, but it should run well. I assume you have checked for a weak spark?