on the intake manifold, there are two plugs that are exactly the same. switch these two plugs around and see if this solves anything. Also try turning the fuel pressure down a bit, it maybe that you are getting too much fuel, are you getting any back fires or anything like that? does it idle perfectly? there should be no hesitation between cylinder fires. make sure that the timing belt is not a tooth off, yes there is room for the belt to be a tooth off both ways. the computer doesnt have to "learn" anything, it non-variable, unless you have a chipped ecu. what rpm does it idle at? just a few thoughts, get back to us and let us know the outcome of these ideas.