I left the EGR as it was, which is blocked with gunk, hence my rough idle and flat spot on acceleration.
I simply backed up my current ECM, and uploaded the new one (HrastProgrammer's 513 EGR/FCV delete - stock).
Yeti from lostjeeps advised:-
"in this file the FCV remaining always open , but it will close at shutdown .......and reopen , like normal operation , and the EGR is always off , this allow more boost to entering inside the intake manifold"
http://www.lostjeeps.com/forum/phpBB...0247&start=700
I read all 36 pages of that particular forum, before I worked up enough courage to do this myself.