By "all the small black pipes", do you mean the breathers and vac lines?
The small box on the back of what would be the passenger side (LHD car in USA) is the breather box. (with the two short pipe/holes coming out the top?)
These may well be blocked, try cleaning the holes out (I used carb cleaner and drill bits, and a paperclip for the small hole). This will let the engine breathe and relieve pressure, which may be why you're getting so much coming through the filler neck. If you can, it's prob best to find some hoses and connect them back up to the breather lines on the plenum (which you should also clean out).
It's prob not ideal to run without being connected, but I'm sure it will work. Defo better to have the holes open than blocked completely.
There's a great guide in the Maintainence section. (You won't need to take the breather box off unless you're really keen, or have the engine out etc)
You gotta wonder why the valves bent in the first place too.
Has the timing belt been done "properly"?
Also, for idle problem, check Idle control valve. It should have a air line to the air intake and another smaller line going to the FPR I believe. You can also clean it out a bit with carb cleaner. (don't forget the ECU connector for ICV too)
You can also adjust the minimum closure of the throttle too, at least you can on mine, with a small nut/bolt that you can screw. The more you do this, the more it will bypass the ICV and it will idle higher, so not recommended by most.
Also, sounding like a deisel? = low pitched? Perhaps you have an exhaust leak somewhere?? (friend hold a rag over the tailpipe and you start her up and check for leaks)
I'm still learning too, but I hope some of this helps
)