I had the similar problem for some time on my 1996 2.0L LX (63,000 miles) and after spending a lot of monies of the cleaning of injectors, changing of spark plugs and plugs wires etc. I eventually discovered that the problem was the engine mounts. Three of the mounts were completely shot (the folks a Ford should be given an award for making the weakest motor mounts ever) I replaced them and the car now runs vibration free.
I would suggest you have your mounts checked.
VBos
