I think, it will work, not but well and your check engine light will be on.

The ECU for the automatic will be looking for input from an auto tranny that isn't there. And, the ECU will be looking to give signals to an auto tranny that isn't there.

Someone correct me, if I'm wrong. But isn't the Toyota automatic tranny computer controlled?....like for shift points? That's why I think it's a problem. And, if you leave any of the "extra" wires just hanging there, your "Check Engine" light will almost definitely be on. And I'd think that your ECU will not be doing it's job of controlling the engine controls (mixture and timing) if it is not getting all the inputs it's suposed to.

If I were you I'd go to, or call up a wrecking yard, and see if you can swap that 99 "auto" ECU for a 99 "manual" ECU. They'll probably charge you something, but I doubt they'll charge the full price. All you have to do is match the year (I'm pretty sure a tacoma, or T100 ECU of the same year and engine will work). Mine has the year stamped on a sticker, on the ECU. And, then you can sleep well at night.