I'm guessing you also have a front pipe in there? To have an after market dump and cat back with stock front pipe would be weird.
It's not an increase in lag you get from a bigger intercooler it's an increase in response and yes it is real. Most R34's don't gain any power from a fmic alone.
That said, if you are upping the boost at the same time then the increased power will make up for the decreased response.
I'd say get a PowerFC and a decent electronic boost controller. If you do any sort of motorsport then get a front mount too otherwise save your money for when your coils die, which they will, and some new iridium spark plugs.
Don't forget to drop the plug gap down to 0.8 when inceasing the boost.