When the ATX is in limp mode, it's stuck in second gear. This is caused almost exclusively by slipping, a bad input speed sensor, bad output speed sensor, or bad range switch.
What manner of "shift box" are you trying to install?
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'95 Eclipse TurboGS (garage deco) '95 TSi AWD (restoring a survivor) '97 Talon ESi-T (poor impulse control) '99 Eclipse RS-T (daily beater) '13 Evo X (mostly stock) '17 Sienna (Middle Aged Dad Mobile)