Engine running bit weird, how to proceed?

Fazer Fail wrote: opened up my ECU the EPROM has yellow sticker PA07 anyone know what that is?

yes it's a red plastic valve, seemed rather cheap to be honest (not just owing to the fact it failed on me). Have ordered some generic ones from amazon as I don't quite see the point for ordering that thing from the Aprilia dealer for €40, but maybe the new part is better? 
Well with the check valve in place, with the vacuum lines as installed on my bike, it seems to me inevitable that the rear cylinder will suck a significant (6mm tube's worth) amount of air through the clutch actuation circuit at idle and near-closed throttle. Perhaps the diagram there shows a different setup to my bike, but what I'm seeing is closer to this general schematics:
-vacuum port above TB ----------------------\
                                                                |
                                            3way-junction>----------Clutch
                                                                |
-vacuum below TB--- check valve (<-dir)---/

So to say, with the check valve actuated at closed throttle (as the pressure at above TB and clutch is clearly much closer to atmospheric than right at the intake port where the engine is trying to suck in air), what is to prevent a 6mm-hose-worth of vacuum to continually pass from the "above TB" port to the "below TB" port, bypassing the TB? Or to put it different, am I missing information/insight, or some parts on my bike?

Ah ok, I guess there was indeed an insight missing - the misunderstanding is in how that "above the throttlebody" port is connected - to me it looked like it just taps into the air column. If you tell me it's indeed blocked off any time the the throttle is closed and that part of the diagram were the air flows through the throttle axis is not just coincidental, that should take care of if all. I'll also try installing dual-check valves (arriving today) as right now that clutch actuation turns out a bit of a curse, quite clunky indeed, lots of force required, and often impossible to get her into neutral with the engine running at a red light. Looking forward to the bike running, shifting and idling as it should, hopefully I can make good use of that rare october sun we have right now...

Thanks a lot for all your help!!

Haha I think the clutch is back on track - did the dual check valve modification as I ordered a 2x pack anyways, and (as far as I can tell with my previous problems) it actually feels quite good and smooth when shifting, clutch force is definitely improved and I can easily get into neutral at traffic lights...