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An auto ECU will run a manual car. Being OBDI, I don't think the ECU even controlled the transmission yet in which case there isn't really anything special about its being from an auto car. The later model OBDII ECUs eventually took full control of the transmission doing away with the separate transmission control module, but even they will run a manual car albeit with a perpetual check engine light for the missing feedback from the transmission. Since you plan on chipping it anyway, I don't think the CIL will be an issue for you either way.
 

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You shouldn't have a problem then. If memory serves, all of the transmission-related connections to the ECU on the later model OBDIIs are on the same connector, so you just won't be connecting that one. I ran an auto OBDII ECU with a manual transmission for years. Other than the CIL, it ran just fine. The one thing you'll probably have to check up on is confirm if any inputs need to be jumpered so the ECU thinks it's in drive. I don't know if the OBDIs do it, but the OBDIIs won't let the engine rev above something like 3500 or 4000 RPM if they don't see the D input. I don't have a wiring diagram for the OBDI ECU to check though.
 
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