So it's all done now but there were a few issues and i'll leave some notes.
Cleaned it all up and slapped it back together and it leaked from the trunion (bit between water pump and oil cooler). Pulled it back out and pulled the trunion out and greased it and assembled it back together and it's all good, no leaks.
So now here are some notes.
You do not need to take the belly pan off, nor the front pipe etc. When I took it apart for the 2nd time I left everything in place.
You need to pull the airbox out, then the bracket next to it that holds all the cable plugs etc.
You need to get to the bloody bracket that ties the intake manifold to the block, you need a #10 (from memory) triple square tool there or spline or whatever they are called.
Once you remove the bracket you take the rubber joint between the throttle body and front pipe off, it just slides once you use a pick to break it free.
Thats it, now take all the bolts off and unplug all the sensors, undo the oil filter, undo the 17mm nut that holds the high pressure fuel line to the pump and some other manifold hoses like the charcoal canister and PCV and you're good to go.
Once the manifold is out you take one bolt off and take the pipe that goes in the middle of it out, this pipe goes to the DSG oil cooler, once that's loosen it just pops out, then you take of the water pump cover (two bolts) and use a pick to slide the water pump belt off, it just slides off easy, undo the rest of the bolts and she is out.
When you put it back make sure you grease the trunion and you can put the belt 1mm onto the flange before you put it back in and then just slide it back (the belt). Keep in mind the trunion has to be placed properly and greased or it might leak.
Then you just do the reversal. I left all the injectors in the manifold and used eyeballed them in line before putting the manifold back in then just use fingers to jiggle them if they don't fit, took about 2min to get them all in.
Also a good tool would be a water bottle cap thingo to pressurise the system and check for leaks before you put the manifold back on.
There is a thermostat in the line that from the big hose that goes to the top of the radiator to the DSG oil cooler, when I had a look the thermostat wasn't sitting in properly from new.... the trick here is to remove the hose from the thermostat and fit the plastic housing of the thermostat to the radiator hose first then slide the hose from oil cooler to themorstat on as the thermostat housing has a spring and it's not easy to compress and put the wire in to lock it. If you don't have a DSG then don't worry about it, that oil cooler might not even be for the DSG, **** knows, it seats next to the battery on top of the gearbox.
I guess if I have to do it again I should be able to get the manifold and pump off in under 40min, clean the intake and valves for 4-5 hours at least then re-assemble in 45min. Piss easy job once you done it once (or twice). I read some how to on the "internets" and in hindsight I shouldn't of as you don't have to go under the at all, let alone take the front pipe off and auxiliary water pump off and other crap.
I think you just need a T30 and 17mm for 90% of the job, add the 10 triple square and possibly pliers to get some hoses off.
After working on this thing.... I will never buy another VW or anything from the VW family again. Nobody in their right mind would make a water pump out of plastic. Half the hoses in the front of the engine are plastic as well, those things will eventually crack and fail. The amount of design flaws in the MK6 is quite big and with the MK6 GTI being cheaper then yeah more corners were cut for sure.
Oh when I started the car (front wheels were lifted off) all sorts of crap came up on the dash, like error with traction control, some steering wheel icon turned yellow, and all sorts of other errors. With the car started and wheels off the ground and in Park the press the brake green light was on and sometimes blinking. All these went away after I moved the car about 5meters. Stopped and started the car again and all good.
next week i got the 100km ride to the bay, the week after will do the DSG service, looks pretty simple
PS. I'm eyeballing a 2016 STI now, surely the EJ25 don't have a lot of plastic stuck to the engine
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