No, you can use those heads with that
ECU, you just won't be able to use AVCS. You may have to add a cam sensor to the front of the passenger side head depending on where the heads came from (i.e JDM/ADM) If you want to use AVCS then you will have to change your
ECU yes.
Not sure on the cooler piping, though there is usually a flexible connection between the TB inlet and the piping, so this might be able to be changed to suit. Either way, it shouldn't be a massive modification if your using a front mount. If it's a top mount your using just use a GD STi top mount and you should have no issues. Better yet, if its an STi one, why not just sell me your GD manifold?
I'm not sure how your SMC will go with the GD manifold, though you shouldn't have any issues as I think the MY98 used a solenoid idle control anyway.