mines not in the car so I can't get that far so can't see what it could be. but as I say don't use the scope as it limits what you can see. Go for measurement blocks which will let you see 12 or so sensor values.
you then get to select the controller you want, either engine or abs. there will then be a button to check fault codes. on the shareware versions you are limited to one measure on the scope. you are better off using the 'measurement blocks' from within each controller screen. which should let you select up to four blocks. each block then shows 4 'random' measures. You can log this to a CSV file and graph in excel or openoffice calc.
don't do an autoscan. that goes and tries to connect to 256 odd modules. a mk3 has 2 / 3. engine, abs and transmission if it's an auto. Use 'Select control module' instead. strange 409.1 didn't work for you. it's the one I'm running with the same/similar lead.
lest we forget, and 'cos I promised Donna I'd reprise it an every possible situation: http://www.vr6oc.com/e107_plugins/forum/forum_viewtopic.php?158187.post
the manifolds are all plain, except a very very few very very early, like development early, ones. the writting is on a plastic cover which come in VR6-DOHC or VR6-2.8 varieties
if it's still on standard suspension you'd be better throwing your money at that so you can make better use of what horse you already have around the twisty bits.