If it was running completely fine before running out of gas, I'd say something needs resetting. Did you work the throttle from under the hood with the key on? That will put you in limp mode. Try clearing codes, and depressing the gas pedal fully with the key on/engine off. If nothing else is wrong, that should get you out of limp mode.

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1983 380SL
1995 C280
1995 S500 coupe
1990 Mazda Miata
2004 Suzuki Hayabusa