Steering / Suspension Noise

I've noticed a bit of front end creaking noise ever since the motor and trans were put back in. It kinda sounds like metal fatigue noise. Hard to explain but similar to the hood opening and closing.

It does this occasionally when turning the wheel and I can kind of feel it on the floor (almost like a slight creak / pop sound). It has also done it when coming to a stop going straight. It just creaks here and there and I can feel it.

None of the steering or suspension was disconnected ever but the car was on the lift for a while with the suspension flexed down. The very top rubber one on the drivers side near the wheel looked like it wasn't connected all the way with the car in the air. Is this supposed to be sealed with grease?

The shop said some of the parts looked good or replaced recently. Here are some pics. Any help is greatly appreciated.