Intake manifold swapped now rough idle

Does it run OK above idle? How long have you been driving it since the swap? The PCM may need to relearn the idle trims:

[wmburns]Once it's warmed up to operating temp, let it idle for one minute with A/C off and the one minute with A/C on [/wmburns]

Simple Green shouldn't have hurt the injectors, assuming the electrical connectors are not still wet. I think I sprayed mine down with SG to get the gunk off before I soaked them in injector cleaner.

Most likely cause would probably be a vacuum leak - NPI means at least 12-15 year old vacuum hoses and lines and you touched them all if you're swapping an intake manifold - check them all thoroughly for cracking or rotting. Those thin little hard lines get brittle and can break or crack too.

Did you replace the gaskets? If not, were they still in good shape - not crushed or deformed, cracked/torn, still pliable? Did you torque the manifold and throttle body plenum elbow down in the correct sequence and to the correct in/lbs values? That's another good source of vacuum leaks after a manifold swap.

An ignition issue could cause a rough idle too - any coolant, cleaner or water get in the spark plug holes? Are all the plug wires seated solidly - double check, they can fool you in those spark plug holes.

^^

What he said, Bear in mind the inlet manifolds from PI sn95s are plastic so don`t go overboard with the tightening of the Plenum bolts. Is there a good seal between the Plenum and manifold? Did you use a sealant?

Always good practice to replace gaskets when swapping those. A gasket is normally good for one torque down. After that they ate crushed and may not perform properly.