Running rough
 

I have just installed a K27 on my 3.3 and up to about 2000 rpm it seems to want of a better word stutter after that it seems to clear and run smoothly .
I have changed the plugs and had the AFR checked the only thing that showed
that it was marginally rich at idle after that it was fine.
Any ideas ?

vacuum leaks
 

Any chance there are vacuum leaks when you changed the turbo out, o-rings, rubber couplers between the piping, or wiring to the IC?

If nothing was touched for years and this is all that you did, you may have disturbed something and caused a crack to become a tear... The K27 should not effect whether the car runs smooth or rough if everything else stayed constant.

Start there.

Bryan