Runs Really Ruff in Drive

Replaced all vacuum hoses, plugs and wires, fixed all electrical and engine runs really good. Real smooth until I put it in drive. The engine starts to run like its running on 4 cylinders. I have the car on jack stands and haven't cleaned the gas tank yet. The gas is supplied from a 5 gal. can under the car. its only regular gas (89) but I wouldn't think that would be a problem. Tran goes through all the gears fine but the engine runs real ruff until I put in neutral and it gets real smooth again. Could it be the trans vac line? Its the only vacuum line I didn't replace. I found it on the tranny but couldn't see where it went on the engine. Any ideas?
 
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