DIY help - ER34 - 1998 RB25DET Neo - Auto

[r34turbo]

Need some help with my Skyline (1998 R34 GTT - Tiptronic - 4 Door - RB25DET Neo Motor - No Mods only Air Filter)

 

Picture 1: What is this box containing a circuit board in my drivers side foot-well?

Picture 2: What is this bolt hole for, does it require a bolt or is it not necessary (could it be creating an exhaust leak, or just housing bolt?)

Picture 3: Is it normal for this to get extremely hot? Could this contribute to rough idle/flat spots at low RPM

Picture 4: What is this wire supposed to connect too, as it is connected to Picture 5 which looks irregular

Picture 6: When unplugged rough idle "mostly" smooths out, however acceleration gets choppy with a massive power cut

 

Also having an idle problem, 

- Rough Idle

- Flat spots and near stall at low RPM - mostly when accelerating from a complete stop or crawl

- When I sit at lights in drive with my foot on the brake, it jerks a little and sounds rough (Idle sits around 800)

- Seems to have majority of power under load but it's hard to tell I don't hammer it

- Exhaust sprays tiny specs of black liquid onto ground in tiny amounts on rare occasions

I will try upload a video of the exhaust so you can hear the idle.

 

I have replaced the air flow meter recently and changed the fuel filter

Advice would be greatly appreciated, I am still learning as I go

running rough.mp4