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A manual transmission has pairs of input/output gears that are constantly intermeshed but normally disconnected from the output shaft, and dog gears that are actuated by the shifter to couple each pair to the output shaft when appropriate. An automatic transmission contains a sun gear, planetary gearset, a system of clutches, and a fluid that cools the transmission as well as providing both lubrication and friction for the moving parts. When the shift selector is in each spot, electronics and hydraulics cause voodoo and magic through direct hydraulic passageways to valves, openings, and dead ends that were included by the designer to make i8t more difficult to escape. Those wonderful "manumaitc" transmissions are just automatics with manual control over shift points and high end cars have sequential manual gearboxes that don't require you to touch a clutch pedal and are essentially the unholy marriage of a manual transmission and a retractable pen.
What it looks like you want to do is to turn a manumatic in to a simulated manual through actuation of an extraneous pedal and control systems including logic circuits, pressure switches, and that superfluous pedal to channel the voodoo and magic into the right hydraulic passageways. You'll also have to program and burn code to sets of ICs and run servos to replicate the actions of the shift lever that you disabled when you disassembled and reassembled it in a different pattern.
It's not practical.
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