Depends very much on the merchandise.

- Does anyone know what's the best method to transport this equipment or can suggest transport companys?
Are the goods especially heavy or voluminous? Any dangerous goods in there?
Usually within Europe you have the choice between Truck and Airfreight, in random cases even by Rail. Transport companies in Switzerland are a plenty...

- How this should be dealt with in terms of customs & border authorities?
What are the conditions and the value? If you have to get the goods to different countries for repairs, improvements or simply for exhibitions, one would usually issue a CARNET ATA, for temporary import in the different countries.

Suggest you contact your in-house or usual forwarder and discuss - they will come up with solutions and ideas. It's their job after all...