Problem is, most of the FTO's are A/T, would the ECU work properly if mated to a 5 speed RWD M/T?

Yes, looks like wiring will ba a hell to work out! hehe...

In the case naman of a SR20DE engine, puede from A/T to M/T without replacing the ECU, advatage pa kasi the A/T ECU will give you more RPM range, tsaka subok na ito.