Do you know anyone else with an RSi? If so you should 'borrow' their ECU and see if it clears the problem. Usually its the coils that cause something like a misfire but if you've already taken them off (shame btw) then the ECU would be my next part to test.
Its unlikely to be the alternator........... but the problem with mk3 Escorts is that the electrics can be a right pain in the arse if a fault occurs. If I were you i'd test the ECU first, see how you get on with that, then if no joy look at other possibilities.

Im sure the lads will correct me if im wrong in any of the above