The game controllers control panel can be helpful for testing that everything is set up. Quickest way to get to it is Windows+R and enter "joy.cpl" without quotes. Then you can test that each axis is working correctly. NB the throttle has three axes for the optional pedals that will not be connected.
There's no force feedback but Thrustmaster's drivers do enable a system-wide deadzone for the analog mini-stock on the throttle, which is very handy. However everything should work just fine without Thrustmaster's drivers.
I second the advice to do without TARGET, it seems to cause nothing but trouble and because it combines both physical devices into one virtual device, it exceeds DirectInput's limit of 8 axes per device so some of the axes get unmapped. In fact it's entirely possible that TARGET has managed to unmap your throttle axis.
Hope this helps.
So I uninstalled all of the Thrustmaster stuff and rebooted the PC. I plugged both the stick and the throttle back in and checked in control panel to make sure all axis/buttons were working properly.
I then went into Elite Dangerous and still none of it would work in Controls. Also there is no option for the T.16000 showing up for me.
http://i.imgur.com/1QvgcdL.jpg
I also went back into Mechwarrior Online just to be sure it was all still working in other games and it worked perfectly there.