If you go auto You will need new axles reguardless of the 4 spd you use.
DO NOT USE THE Stock FIERO 3SPD! it is junk when used with the 4.9
4 spd Manual too short gearing, not well suited for the power band and rpm range of the 4.9.
5 spd Getrag better but 5th is kinda short for the RPM Range.
5 spd Isuzu, Im using and it seems to fit the RPM range well, 1st will be a little short but I will have to live with it.
When using the Fiero Manual trannies you do not need Axles as you use stock. You will need a Custom Flywheel though.