A TD04 is bad, but its not that bad. On a 2.0L you shouldnt be shifting at 5700 RPM on the TD04.
Peak power usually occurs in the neighborhood of 5500 RPM and torque at 3500 RPM IIRC. But you don't want to shift at 5500. You would want to run it out another 700-800 RPM to take advantage of the area under that curve. Power over 6500 RPM drops off pretty quick usually (depending on your supporting mods, fuel, and tune) so no point in running out past that in 2nd/3rd but I would have to say its probably faster running 1st out to redline.
Keep in mind where you shift is determined by the shape of your powerband, which largely is effected by your tune. 20 psi should put out a lot of torque. Especially in cold temps at sea level. The higher your low/midrange torque values, the more advantageous it would be to short shift.
A trap speed of 99mph at sea level tells me there is something that's not quite right with the car. Even if your ET isnt the best, the trap speed usually doesn't change much. I would be hoping for significantly faster traps. No huge boost leaks/heatsoak/timing map problems? Running on 19" rims?