For a 4AF Automatic to 5SPD swap, no, the ECU can be left alone. Besides having to change the flywheel, install the clutch and pressure plate, all shift linkages, clutch cylinder, clutch pedal, and the 5spd trans itself, the only thing you have to do is jump the neutral safety switch wire that way your car can start. The trans on 4age should work on 4af/4afe since it's all the same block and stuff. The ratios may be different. I plucked my 5spd from another 4af corolla, so I knew for sure it would work.
If you plan on changing the motor out as well, I suggest (in my own opinion) doing it all one time since it will be easier a bit... if you can.
To swap a carb motor to a fuel injected motor (ie the 4ages'), you'll need to replace the gas lines and maybe the gas tank and install the fuel pump that goes in the tank for efi. Gas stuff can come from an EFI/ 4afe corolla. Other than that, the wiring harness and ecu from wherever you're getting your motor.
I'm not too sure if the silver or black would pass CA emissions. But I don't see why it wouldn't if everything is done right.
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AE92 GTS Skirts | AE92 LE Trunk Garnish | 4AGZE Cryo-Blueprinted Crank
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