Mmmm think I have solved it....Wiretap you are right ill put it to the test tomorrow. I took everything out, Put my old HKS intake in with mushroom filter, this ran fine like it did before I changed anything, now from there i took off the mushroom filter car still running fine with no filter, now from there I put on the K&N filter still running fine and from there I took my custom pipe taped over the MAF plate and connected it to the HKS MAF tube... this also runs fine. So it must be the custom MAF I have done. Tomorrow ill cut the MAF out of the custom pipe and join it all up using the HKS MAF and going by all of the above in should run smoothly....fingers crossed.
Only down side to reusing the HKS MAF tube means it wont look as clean and I cant sell off the HKS intake
Other thing is the MAF is going to be sitting about 50-60mm closer to that bend in the black standard piping, I'm hoping this will be alright.