As David has said, without any logging it's hard to advise on anything.
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As covered in the help, you can see how the each phase of the shift implements various settings.
The goal of the Preshift is to generate negative torque to allow the dogs to unload, and to charge the inlet with air (which on a short runner ITB setup isn't a large volume, but it can quickly draw air from the plenum.) to allow for a crisp blip.
For this to all work correctly, you need to be running enough ignition cut or retard to minimise the engine making power during the blip. As you have an S54, I would avoid excessive cut if you plan on keeping the shims where they belong. If you are not doing enough in this regard, the engine will accelerate when the blip occurs. You do not want to use fuel cut however, as you will need the fuel film present to ensure the blip is works when the gear shift state changes to shift.
Depending on your actuator settings, your shift actuator is activated before the gear shift state changes to "shift". This is determined by the gear shift actuator timing.
Once the "shift" phase begins, the retard and cuts are removed, allowing the engine speed to increase, whilst if the timing for everything in the early stages is correct, the actuator should be helping the gearbox start engaging the next gear. If the engine does not increase in speed quickly (provided you don't have any filters on your pressure sensors) you can take a look at the lambda for an indicator if there is enough fuel present.
Post shift is then used to help being the engine speed back down before the recovery phase to re introduce torque. Depending on if you are using gear shift engine speed limit mode or not will vary what your trying to acheive here, but the main purpose is this helps "catch" the blip to help match the engine speed for when the recovery phase occurs.
As you are working with shifts where everything can occur in well under 100ms, you need to log things as fast as possible. Gear shift state, Gear Position sensor, Throttle Servo Position, Throttle aim state, Ignition timing, Engine Speed, Inlet manifold pressure, fuel and ignition cut average along with paddles, actuator duty lambda and everything else are needed to determine what changes are needed to improve shift quality.
As you have an ITB car, my first instinct is that your air/fuel balance is not allowing the engine to blip cleanly. Commanding a massive blip with that much throttle area will need a lot of fuel to make the engine respond, otherwise you will find the engine runs lean during the shift phase and splutters.