I had a failure of the STVA on my 04 600 mid-session earlier this season. Joe from Turn One Racing told me to open the butterfly valves all the way and disconnect the STVA electrical plug.
A fellow rider had a similar failure, and found that his bike (a 750) was limited to 5000 RPM. I believe that it is the reported position of the butterfly valves when the ECM loses communication with the STVA that determines the failure mode.
I rode the rest of the day with the STVA disconnected, and the main thing I noticed was that the low RPM (3-6K) torque and acceleration was less than normal. It made it a lot harder to drive out of tight corners.
I found instructions on-line for fixing the actuator, and performed the repair, which returned the bike to normal. I also found mention of a device that emulates the STVA that you can buy to plug into the end of the harness to keep the ECM happy.
The repair took about an hour and cost less than $10 in parts, mostly the screws, lock washers and nuts needed to re-assemble the STVA after drilling out the pop-rivets that hold it together.
However, I don't believe that it hurts anything to leave it disconnected. You will just have any additional failures or codes masked by the continually lit FI light
