Are you sure there's not already a spacer in your new cylinder? Previous research seems to suggest that your pushrod should be 335mm so you wouldn't need the spacer. I think from memory the cylinder comes from Oberon with the spacer fitted and you had to remove it if you had the longer pushrod.
Also, does your pushrod have the anti-rotation pin? If so, perhaps it's not aligned with the slot in the slave cylinder - that would prevent it from seating properly.
Plenty of pushrod information here:
http://www.ukmonster.co.uk/monster/s...ad.php?t=56050
Regarding the "quiet clutch mod", I assume you mean this one:
http://www.ukmonster.co.uk/monster/s...ad.php?t=56305
http://www.ducati-upnorth.com/forum/...iet-Clutch-Mod