I'm assuming you're checking the vacuum reading with a guage and not be ear? A good vacuum guage will tell you a lot about the condition of your engine. What Hg are you pulling with the car in neutral? How does that change when you plug the tranny modulator line?
just two things to consider
First, if your vacuum is changing AT ALL when you plug up the tranny line, then you have a problem. If your system is working properly there should be no change with hoses connected or disconnected. Check the line at the end of the tubing to make sure that's OK, then check again when connected to the modulator. If you have a change, you have a leak.
Second -- are you sure you have your idle set properly? The car should be 600 - 650 in DRIVE (about 900 in neutral). If you set the car to idle at 650 in neutral, you're going to have problems and run rough.
Good luck!