Pulsing brake paddle

I would think that to trigger the ABS pump, one of the wheel sensors should first give a signal to the ecu / pump.
And as it does not happen all the time, the fault sounds like an electronic one.
As far as I know the sensors are not very expensive, maybe start with replacing them first if nothing else comes up. Or start with cleaning them, or checking if the connections and wires are still ok, after that disc and pad change.

 

There are 3 parts that will go sooner or later on the 355 brake system. You have to take off the moulded carpet pieces in the front luggage area to get to them all.
There is a brake relay on the passenger side near the top of the area under the carpet. This relay is not very expensive. Then just below that attached to a block on the brake lines is a grey brake pressure switch...part number 154309 a little more expensive but well under 100 bucks. Then there is the pressostat attached to the ABS pump on the drivers side. Ferrari does not sell this part alone but somebody on Ebay does. Unfortunately it is very hard to tell which on of these is the culprit so I would start by replacing the first 2 cheaper parts.

 

Were brakes bled?

 

this....the ABS sensors could have picked up oil/grime while the disks were changed....or they could have lost a spacer and are closer than they should be with the rotors..... the sensors themselves can be easily removed and cleaner....start with this first....

 

Nope I would start by bedding in the brakes. This is never necessary on streetcars with street pads. On occasion someone uses a hotter pad. In fact Ferrari uses a harder skeaky pad in at least 1 version of the 550M as an example. It is possible that after you bed in the brakes and get a good transfer layer those sensations will be gone. You got nothing to loose by giving that a try plus it is really easy. Sometimes on a racecar you can get the sensations you report when switching pad compounds on old rotors.
So sometimes you have to bed-in and sometimes not.