ok mate, i think you really need to dig through the FSM's a bit more and look at the wiring of Plugs B137 B135 and B136
these are the plugs for 3pin ECU which you have in that photo..
can you clarify what you are doing exactly?
taking the manual box from a 2.5 RX ?
and putting it into a 2.2 GX ?
Wiring Diagram.pdf 5.24MB
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Page 60 should be your 2 plug ECU from your GX auto in the first PDF
Cross reference it with the info in the second PDF..
conversion19.jpg 134.55KB
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ignoring the turbo stuff..
im pretty sure all the Auto stuff is self contained in the TCU (Transmission control unit) the only reason anything connects to the ECU plugs is due to needing VSS input and Revs.
so most of that stuff probably just is a feed from the ECU but not actually vital once the TCU is removed...
i'll try dig up my sheets i made when i did my conversion as i mapped each plug in the 3plugs for the NA 2.5.. but really.. i think i only added the turbo stuff and some common grounds.. everything else i think stayed the same.
just read through that first PDF a bit more and trace each wire from the ECU and see where it needs to go...
this should be alot simpler than you think.
sounds like your just going in thinking its going to be harder than it should be.