I did this swap earlier this year, the composite does improve performance over the aluminum upper--used half-shafted stock TB's on both. Use the 99' lower and drill out the sleeve on the composite upper. Delete the EGR--remove the DPFE, EGR valve, EGR Tube and the EGR solenoid at the rear of the manifold. With little work to the 02' TC bracket the 99' TC will work. You'll need the newer intake tube if you plan on using the 02 TB, the newer tube doesn't have a IAT sensor hole--I relocated mine to the airbox.
Here's a link to a thread I started on another website when I did the swap.
http://www.ranger-forums.com/2-9l-3-0l-v6-tech-32/finally-installed-my-composite-upper-133037/
Shortly after the swap I drove to Seattle and back, about 220mi each way and averaged 23mpg highway. This is through a lot of mountain passes and cruising at 75-80mph down I-90. Not bad for an ex-cab 4x4 truck.