I cleaned all the pipes and O rings on the pipes all around from the turbo to intercooler back to EGR valve.
There wasn't much gunk just some oil.
Fitted them back and all the fittings were pretty tight so I don't think there was a need for new O rings.

I'll get a mate of mine to do a scan on the turbo boost sometimes this week or next I'll post the results here.

I'll have a look at the alternator bolts as well to get the noise down.
Mind you currently its far less noisy than non PD 1.9 I had in the past.
 
Just an update on this

I followed this guide: https://www.youtube.com/watch?v=56oIU-sF7d0

Basically took the exhaust pipe off the turbo and checked for play in the vents.
There was no play whatsoever so I'm glad I don't have to replace that.
Had a look at the actuator and it didn't move as smooth as I though it should have then I sprayed Mr Muscle into the turbo as shown in the guide. It done the job it is boosting better now.

Im still not 100% happy, I think my old 1.9 TDi SE non PD was pulling better... so next up is to replace the vacuum lines