R9 Pilot Guide is on avidyne.com select Support, them select Pilot Guide.

I would like to understand how best to update the databases.
---- The Data Base Updates are obtained, by subscription, from Jeppesen.  Jepp Direct [Sales/JDM] 800-353-2107  
       You will need an 8GB USB thumb drive formatted to FAT-32
        Be sure to inform Jeppesen that you have SW Rel. 9.4.x

Is there a software upgrade to install beyond 9.4?
---- 9.4.x is the latest software for the display of FIS-B IN DATA.  There is a Rel. 9.4.2 but its only change was the addition of a G-Meter for a customer using the system as a Military Trainer.

I see two OAT indications on the panels - one on the PFD, one on the MFD. They read different temperatures, whether the temps are warm or cold. Is this normal? Are there 2 sensors? Which one should be treated as primary? Which one is feeding the flight system and being logged? The difference can be as much a 5degC.
---- There are two (2) independent Magnetometer/OAT assemblies located in the right wing.  The two OAT Probes are on the bottom of the wing just outboard of the landing gear. 
---- Have you local Avidyne Dealer check the system to determine which one is operating correctly, and then have them make arrangement to have the faulty unit exchanged.

When I examine the logs, I see no data being populated for ALT1 and ALT2 currents. Is this as expected?
---- The ALT1 & ALT2 currents are not shown in the Pilot's Logs. There are two (2) additional hidden Technician logs, Events & Volts , which your local Avidyne Dealer can access.
---- These logs are a useful tool in troubleshooting.

How should I expect the installed ADSB in-out to display? I see ‘Datalink not received’ and ‘Datalink Error’ messages, or similar in green on the MFD. How can I test that this is even working? I see no FIS-B and no obvious traffic. However, I have never flown closer than 100nm north of the nearest ADS-B tower and possibly too low to see them… 
---- Your Aircraft is equipped with an L-3 SkyWatch ACTIVE Traffic System.  It does NOT make use of the TIS-B ADS-B IN Datalink Traffic.
---- The Skytrax-100B/200 Datalink Receiver is used you receive FIS-B ADS-B Weather data only.  To check it's Status go to the Sensor Tab_ Sensor-Datalink_Datalink -Status, The Service Level should be "ADS-B WX"

I see a note on the Map screen stating ’No traffic Overlay’.  What does this mean - i.e. is there a fault or would I not expect an overlay on this screen in certain configs? When the traffic sensor is operational (see Failure1 below), I do see indication of traffic in the HSI and the data block, but not on the map. Is there a setting I am missing?
---- Since Traffic is displayed relative to the aircraft, the MAP Setting needs to be in "TRACK UP”, NOT "North UP" to Display Traffic on the MAP Page
 

Are status code (status flag) decodes available to assist my analysis of the various logs? eg 0x10000 for DFC100 status
---- 0x10000  = ApReady 

I see no record of the MFD alerts/messages and their acknowledgement being recorded into the logs. Is this expected?
--- As in Q4.. the alerts/messages are logged in the Events Log

Pitot Heat Required warning message - I have experienced this message being presented multiple times, even after I have indeed switched on pitot heat. Is this alert linked only to OAT and is not looking at the actual pitot heat status? If not, I guess it could have been that the (an?) OAT was oscillating around the alert temperature, hence the multiple warnings.
---- The system monitors the OAT's and determines the need for Pitot Heat. The system monitors the condition of the Pitot Heat Switch (Current) and should eliminate re-occurrence of the warning.
---- There may be an issue with your OAT Sensors as asked in question Q3.  The Events and Volts Logs with show any discrepancies.  Q4.

Issues:
Failure1. After approx. 30mins of flight (can vary from 15-45 or more and does not appear to be altitude or OAT dependent) the traffic sensor fails with a green message and a red ‘x’ across the data block. It always works on the ground. Fails after some time in flight.
---- If your Traffic System is the Active L-3 SKYWATCH.  Have your technician check the operation of the Skywatch SKY-497 Processor.

Failure2. I receive green alert messages relating to the ‘Datalink’ non-reception of data and failure. Is there documentation on the integration of Skytrax 100B/200 and R9 and these messages?
---- The DATALINK "Data Not Received" is caused by the lack of reception of an ADS-B Ground Station. (normal occurrence while on the ground)  
---- The DATALINK "Failure" is a fault in the Skytrax-100B/200 or associated wiring.