GTR 2 works well with Windowed Mode A or Limelight and TrackIR tracking. You can use Vireio Perception to receive a fake 3D image. When using Perception the cursor will be at an offset in menus but you can still navigate them.

To get TrackIR working correctly you have to edit your profile:
Open GTR2\UserData\<name>\<name>.plr

Set these values:
[ Controls ]
…
HMD Pitch Exponent=”0.00000″ // Exponent to apply to pitch tracking. > 1.0 makes tracking near-center slower, > 0 & < 1.0 makes tracking near-center faster.
HMD Yaw Exponent=”0.00000″ // Exponent to apply to yaw tracking. > 1.0 makes tracking near-center slower, > 0 & < 1.0 makes tracking near-center faster.
HMD Roll Exponent=”0.00000″ // Exponent to apply to roll tracking. > 1.0 makes tracking near-center slower, > 0 & < 1.0 makes tracking near-center faster.
…
TrackIR Pitch Down Limit=”-1.00000″ // Min: -1.00, Max: 0, Default: -0.15
TrackIR Pitch Up Limit=”1.00000″ // Min: 0, Max: 1.00, Default: 0.05
TrackIR Yaw Left Limit=”-1.00000″ // Min: -1.00, Max: 0, Default: -0.40
TrackIR Yaw Right Limit=”1.00000″ // Min: 0.00, Max: 1.00, Default: 0.40
TrackIR Roll Left Limit=”-1.00000″ // Min: -1.00, Max: 0.00, Default: -0.075
TrackIR Roll Right Limit=”1.00000″ // Min: 0.00, Max: 1.00, Default: 0.075

If you have to reset TrackIR ingame use Trinus Gyre’s reset hotkey not the one from GTR 2.

However, TrackIR roll seems to be inversed for me. Can someone confirm this?