The usual suspect is the line from the intake manifold to the ALDA, but you say that it doesn't even rev in neutral. You don't need boost or a boost signal to the ALDA to rev in neutral.
I take it you didn't alter IP timing. No reason to touch the IP when removing the intake manifold.
You didn't mention undue noises, vibration or smoke so I assume the fuel system is bled. It's self priming so it should sort itself out by the time the engine catches.
If you would indulge me, remove the crossover pipe and see it revs more freely in neutral. Your sucking unfiltered air into the engine at this point so pay attention to what you;'re doing.
Then pull the ELR connector from the back of the IP and see if that changes anything. Expect the idle to drop but it should stay running on its own.