I know im not a technical guy with 5 speed swaps but i have a thread here that will help you
zerothread/181139
Click that link and it will give you a full write-up that is very good and shows in picture form and word form step by step on how to convert an auto-manual swap on an S13 convertible.
Hopefully you will find your answer in this write-up i am providing you.
Also if you are having trouble wiring your car then here is a link that will help you
http://www.ka24development.com....html
Its for an S14 wiring but im sure it will be just the same. If you are still having trouble then here is another one
zerothread?id=77784
Those are all the links you need to know to do the Auto-manaul swap. Good luck and maybe one of these threads will answer ur question