I agree with Lozza on the plug heat range, the 10 may be a bit too cold and causing intermittent fouling. I'd also think that it may be not breathing all that well, you mentioned you opened up the porting, although 4mm lower on the inlet does seem a bit extream but it may want more exhaust flow so I'd be looking at the pipe as well.
From memory the PE pipes had a restrictor mid section in the standard pipe, you may have to look at removing that to let it flow better. There is some information on this mod in one of the manuals for PE's altough I'm not sure which one.
Check all the jetting right from the pilot through to the main and the slide cut-away, but a larger main may be needed particually if you open up the pipe and get it reving higher.