What steps have been taken to rule out instrument failure due to blocked static ports or pitot tubes?
The best thing way to mitigate an issue like this is to draw attention to during the preflight check. Its becoming common to use covers that have a nice big red "Remove Before Flight" tag on them. These should be used as much as is practically possible (storage, cleaning, maintenance etc.)  

Something like this would do nicely. 

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Similarly the aircrafts paint may be done in such a way to make the port stand out. 


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Caps/Covers for both static ports and Pitot Tubes are generally a good idea and can help prevent a clog that occurs while the plane is on the ground. As with anything diligence during preflight is key to avoiding this issue. 

Most larger aircraft pilots call out "airspeed alive" during their takeoff roll as a way of confirming the Pitot system is working. If the air speed indicator does not read, the general procedure is to abort the takeoff. 

Some aircraft may also be equipped with a radar altimeter which can help mitigate serious issues by providing an altitude system not based on the static system. However this only works at lower altitudes.