Hey there,
I have a gen 2 I've just taken the head off and gotten it serviced with cams, adjustable cam gears etc etc and a metal HG, also have installed a GT28 turbo kit, boot mounted intercooler and walbro fuel pump. Standard otherwise.
 
It is running alright at idle and I can drive it around with no problems if I stay off boost but once I put my foot down it will get to 2-3 psi then start to bog down and the revs barley increase, boost will climb to 6-7 psi with no difference in power. This is at about 2000rpm.
 
The spark plugs are black with unburnt fuel and there is a small amount of black smoke coming out the back when I rev it stationary, I can't see a huge cloud coming out when driving on boost but I'm sure there's some...
 
I have reseated all the plugs and leads and the timing is fine I also tried another set of plugs which are also black now. Taken all the intercooler fittings off and checked them and reinstalled, looked at all vacuum hoses and they all "look" ok. I have replaced about half of the vacuum hoses while I was putting the engine back together, my next step was to replace the rest.
 
I have also checked the AFM resistance and it is all fine. Not getting any ecu codes. Compression is 160 on all 4 cylinders.
 
Could the new fuel pump cause these issues by itself or could it be something like the vacuum line to the FPR?
 
 
 
 

With all these new mods are you still using the factory ECU? 
Assuming you are, the ECU will have great difficulty catering for all these changes.  You will very likely have to go to an aftermarket ECU.

yep exactly as kojab said, i think too many mods, esp cams and cam gears with the bigger turbo for standard ecu to cope

Check the rest of your iginition components like the cap, rotor and leads.

Cam timing may be off.