I left my auto rear engine mounts in when i converted mine to manual. Whats the difference??
Also the auto shifter cable i cut off cable where it exits the body to save having to remove the exhaust to get at it properly if your time sensitive.
Left all the wiring loom in place and just soldered the wires for the reverse lights and auto safety switch. Left trans TCU in place.
Also did the conversion with the engine in place. Bit fiddly doing the clutch master but doable.
One recommendation is put a new clutch kit in when you do it.
Cheers Vee