I have done this to a Nissan auto. very similar.
you need to wire the inhibitor switch up to some relays and use the relays to switch the autos solenoids on/off. if you remove the auto ecu you will also need a switch to lock up the tq converter ( very good being able to manual it on in some situations like going up hill in 3rd.
mine was set up so that 1st was 1st, 2nd was 2nd, D was 3rd and D + OD switch was 4th, then had an extra push button for lockup.
there will be a line pressure solenoid which drops pressure during shifts. on the Nissan I just left thus wire dc'd which ment much firmer quicker shifts with no slippage.
as far as I know the mech linkage only controls P,N,R and D21. d21 are all the same mechanically and you can access all forward gears electronically while the stick is in any of those 3 positions.
the inhibitor switch is what tells the ecu where the lever is.
all you need to find out is what solenoid combinations do what. it will be something like gear 1 solenoid one, gear two solenoid two, gear 3 no solenoids and gear 4 both solenoids.
hope this helps.