When a microswitch is closed it will be grounded so measuring the resistance between the relevant pin on the STC module plug and ground should be close to 0 ohms, Pin 29 of the STC module plug is ground. Disconnect the plug and start measuring
Main Ram upper switch (fully extended) - Pin 2
Main Ram lower switch (fully retracted) - Pin 16
5th Bow Ram upper switch (fully extended) - Pin 31
5th Bow Ram lower switch (fully retracted) - Pin 3
Cover Ram lower switch (fully retracted) - Pin 18
Windshield Reed switches (closed) - Pin 34 left, Pin 19 right
5th Bow Intermediate switch (this is the position of the 5th bow in the closed roof position, the ram is neither full extended (raised 5th bow) or fully retracted (top fully down) - Pin 4
5th Bow Latch switches (in cover) (closed) - Pin 17 left, Pin 32 right
Cover Latch switches (closed) - Pin 5 left, Pin 33 right
Storage Bag switches (bag up) - Pin 30
So for example with the roof in the fully closed position the following switches should be closed (grounded)
Windshield (both), Main Ram (upper), 5th Bow Intermediate, 5th Bow Latches (both), Cover Latches (both), all others should be open (note the Storage Bag switch will vary depending on storage bag position in trunk).
I would multimeter each switch in a position when it is meant to be open and closed and make sure it matches up.
The top does the following steps when attempting to open, lower and stow away.
1. The 5th bow unlatches (this is electronic), you now know all about this step.
2. The 5th bow raises to a vertical position.
3. The torneau cover will unlatch and raise to a near vertical position.
4. The 5th bow will start to lower.
5. The 1st bow (and bows 2-4) will also start to retract, at the same time the 5th bow passes past it's intermediate position and retracts into the storage bag.
6. The 1st bow continues to retract until it is full retracted and in the storage bag.
7. The torneau cover closes and latches.
Once one step is completed the STC module waits for a signal from one of the various micro switches before proceeding to the next step, if the signal isn't received with in a certain amount of time the system will error and message will display on the SID.
So for example once the 5th bow unlatches (and the 5th bow latch micro switches are open) the 5th bow will raise, the torneau cover wont unlatch until the STC module receives the signal from the upper 5th bow ram micro switch that the 5th bow is fully vertical.
Also the next step can not be completed if there is a problem with the hydraulic system (motor, pump, hoses, rams, valves, etc).
By releasing the emergency pressure valve (and manually unlocking the torneau cover) you can manually move the top throughout it's entire range of motion and measure the micro switches (via the above info) to make sure they all report the correct condition (open when they should be open, closed when they should be closed). If all the micro switches check out then start looking at the hydraulic system, common failures are leaking hoses and rams, but I have also seen the internal seals of the pump leak and the valves not correctly respond to the STC module.
No Tech II should be necessary (though it will help diagnosing the generic "Soft Top Failure" message) for the og9-3 convertible system, the only time it is required would be if you were replacing the valves since they share a common bus they each get programmed to their specific position so they know when to accept a command from the STC module and when to ignore it. If you replace the valves with used ones, then as long as you place them in their original positions they don't need to be reprogrammed.