please do not panic.
You may overhaul the engine with oem new parts. swap only ECU & Transmission.
Visit Faisal in Lines area for such job. Make sure that you know what he is offering as solution - and how much amount he will be adjusting for manual transmission, the clutch pedal.
remember ECU for auto transmission is differen then manual transmission vehicle and wiring need to be configured for shifting. keep discussion open here for input.