RE: 6.1 Manual Shifting issues
It's actually doing what it is designed to do. To help with fuel economy, there are soloenoids in the transmission that lock you out of 2nd and 3rd gear. Its the 1-4 skip shift, and can be disabled with aftermarket euipment, or you can drive it agressively, and then it will let you shift through all the gears. The same technology is used in Corvettes and other vehicles that use the Tremec manual transmission.