One problem related to manual transmission column shift has been reported for the 2006 Ford F-150. The most recently reported issues are listed below. Please also check out the statistics and reliability analysis of the 2006 Ford F-150 based on all problems reported for the 2006 F-150.
Transmission shift cable outer sheath was melted on exhaust system. Cable had unknowingly come loose of a retaining clip and was then allowed to contact hot exhaust manifold. Melted the outer plastic of shift cable causing the shift selector to become inoperable. Shift selector could be placed in park but transmission would not be in park; if I had not realized there was a problem I could have believed the transmission was in park when it was not and the truck could have rolled freely. Truck is a well maintained 2006 Ford f150 crew cab 4x4 with the column shifter.