the knock is probably something mis-aligned, or the bushes need greasing up a little more.
the ECU reset procedure needs to be done after the plenum spacer
the trans probably needs new fluid, or a top up!
youll probably need to do the radius rod/castor arm bushes as they are pretty much all flogged out http://www.m35stagea.info/forum/viewtopic.php?f=27&t=240