If you post the engine number it might help
I can tell the likely hood it came from an Auto car or not, as the early versions in the 90-91 CRX and Civic SiR never came with an Auto option.
While the Xsi and Rsi Integra only had the Auto as an option in 1992.
If its from a 92 on Civic/Del Sol SiR then I believe more Autos than Manuals were sold in Japan, and so it figures that there will be more floating around. However most importers should be honest enough tell you what your getting.
But the easiest way to tell is:
Loot at the ECU. If it has an "AT" printed on the Circut bourd (you will have to remove the cover) then its and Auto ECU and most likely an Auto spec engine.
And even easier way to check:
Look at the flywheel. If the engine has one, and the bolts dont look like they've been recently removed then clearly its a Manaual spec engine.
If it dosnt have a Flywheel, but a Torque Converter or backing plate then clearly its an Auto engine, or if it has a flywheel and the bolts look recently removed then it may be an Auto engine with a flywheel added.
Incase you didn't know the Auto spec engines only make about 150hp. They run milder cams and different ignition timing. As well as a differnt fuel map etc on the ECU.