You have effectively made two changes to the car at the same time, 1) new engine, 2) new intake setup. One of these two things has caused you an issue with reduced output, so you need to decide which path to go down first to work out what is causing your issue. Either there is a problem with the engine itself, a problem with the engine's installation or ancillary component, or there is a problem with the intake system (namely it is too short). I would say it is easier to put the intake system back to standard and rule that out than anything else, so it would be my first course of action. The cone filter is the end of your intake system, there will be no vacuum in the custom feed you have installed because it is not a sealed system.